Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 18:06:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reb_4848/08_2023/6reb_4848_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reb_4848/08_2023/6reb_4848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reb_4848/08_2023/6reb_4848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reb_4848/08_2023/6reb_4848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reb_4848/08_2023/6reb_4848_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reb_4848/08_2023/6reb_4848_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34301 2.51 5 N 9113 2.21 5 O 10174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ASP 73": "OD1" <-> "OD2" Residue "1 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 33": "OE1" <-> "OE2" Residue "1 ASP 69": "OD1" <-> "OD2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 GLU 165": "OE1" <-> "OE2" Residue "1 ASP 172": "OD1" <-> "OD2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 ASP 199": "OD1" <-> "OD2" Residue "1 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 215": "OE1" <-> "OE2" Residue "1 GLU 229": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 329": "OE1" <-> "OE2" Residue "1 GLU 341": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 GLU 409": "OE1" <-> "OE2" Residue "1 TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 425": "OD1" <-> "OD2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 457": "OE1" <-> "OE2" Residue "1 GLU 475": "OE1" <-> "OE2" Residue "1 GLU 499": "OE1" <-> "OE2" Residue "1 ASP 504": "OD1" <-> "OD2" Residue "1 GLU 513": "OE1" <-> "OE2" Residue "1 GLU 516": "OE1" <-> "OE2" Residue "1 ASP 539": "OD1" <-> "OD2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "2 GLU 22": "OE1" <-> "OE2" Residue "2 ASP 31": "OD1" <-> "OD2" Residue "2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 GLU 86": "OE1" <-> "OE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 ASP 189": "OD1" <-> "OD2" Residue "2 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 278": "OD1" <-> "OD2" 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 GLU 420": "OE1" <-> "OE2" Residue "2 ASP 426": "OD1" <-> "OD2" Residue "2 TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 93": "OE1" <-> "OE2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 213": "NH1" <-> "NH2" Residue "3 ASP 217": "OD1" <-> "OD2" Residue "3 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 233": "NH1" <-> "NH2" Residue "3 ARG 242": "NH1" <-> "NH2" Residue "3 ARG 257": "NH1" <-> "NH2" Residue "3 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 276": "OE1" <-> "OE2" Residue "3 TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 295": "OE1" <-> "OE2" Residue "3 PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 64": "OE1" <-> "OE2" Residue "4 ARG 84": "NH1" <-> "NH2" Residue "4 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 133": "OD1" <-> "OD2" Residue "4 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 160": "OE1" <-> "OE2" Residue "4 ARG 176": "NH1" <-> "NH2" Residue "4 ASP 181": "OD1" <-> "OD2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 193": "OE1" <-> "OE2" Residue "4 PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 214": "OD1" <-> "OD2" Residue "4 GLU 225": "OE1" <-> "OE2" Residue "4 ASP 231": "OD1" <-> "OD2" Residue "4 ARG 232": "NH1" <-> "NH2" Residue "4 ARG 255": "NH1" <-> "NH2" Residue "4 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "5 PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 109": "OD1" <-> "OD2" Residue "7 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 117": "OD1" <-> "OD2" Residue "7 PHE 118": "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 GLU 12": "OE1" <-> "OE2" Residue "9 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 40": "NH1" <-> "NH2" Residue "9 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 92": "OE1" <-> "OE2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "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 ARG 232": "NH1" <-> "NH2" Residue "M ARG 239": "NH1" <-> "NH2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 111": "OD1" <-> "OD2" Residue "P ASP 127": "OD1" <-> "OD2" Residue "P GLU 143": "OE1" <-> "OE2" Residue "P TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 166": "OE1" <-> "OE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P ASP 179": "OD1" <-> "OD2" Residue "P PHE 182": "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 ASP 25": "OD1" <-> "OD2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 54": "OD1" <-> "OD2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 62": "OE1" <-> "OE2" Residue "R PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 174": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 83": "OD1" <-> "OD2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "S ASP 144": "OD1" <-> "OD2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T GLU 72": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ARG 96": "NH1" <-> "NH2" Residue "T ASP 112": "OD1" <-> "OD2" Residue "T TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 226": "OD1" <-> "OD2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 389": "OD1" <-> "OD2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "NH1" <-> "NH2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 475": "OE1" <-> "OE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 495": "OE1" <-> "OE2" Residue "T ASP 516": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 72": "OE1" <-> "OE2" Residue "U TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 135": "OD1" <-> "OD2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ASP 326": "OD1" <-> "OD2" 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 ASP 389": "OD1" <-> "OD2" Residue "U GLU 409": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U GLU 455": "OE1" <-> "OE2" Residue "U PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 510": "OD1" <-> "OD2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U ASP 516": "OD1" <-> "OD2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 403": "OD1" <-> "OD2" Residue "V GLU 409": "OE1" <-> "OE2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V GLU 455": "OE1" <-> "OE2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 467": "OD1" <-> "OD2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V ASP 516": "OD1" <-> "OD2" Residue "V ASP 547": "OD1" <-> "OD2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ASP 36": "OD1" <-> "OD2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ASP 82": "OD1" <-> "OD2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ASP 94": "OD1" <-> "OD2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X ASP 139": "OD1" <-> "OD2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 168": "OD1" <-> "OD2" Residue "X TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X GLU 270": "OE1" <-> "OE2" Residue "X TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 348": "OD1" <-> "OD2" Residue "X ASP 359": "OD1" <-> "OD2" Residue "X ARG 366": "NH1" <-> "NH2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X ASP 423": "OD1" <-> "OD2" Residue "X GLU 451": "OE1" <-> "OE2" Residue "X PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 479": "OD1" <-> "OD2" Residue "X ASP 480": "OD1" <-> "OD2" Residue "X TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 505": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 536": "OE1" <-> "OE2" Residue "X GLU 541": "OE1" <-> "OE2" Residue "X ASP 542": "OD1" <-> "OD2" Residue "X GLU 546": "OE1" <-> "OE2" Residue "X GLU 557": "OE1" <-> "OE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y GLU 55": "OE1" <-> "OE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ASP 82": "OD1" <-> "OD2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ASP 94": "OD1" <-> "OD2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ASP 136": "OD1" <-> "OD2" Residue "Y GLU 149": "OE1" <-> "OE2" Residue "Y PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 216": "NH1" <-> "NH2" Residue "Y GLU 226": "OE1" <-> "OE2" Residue "Y GLU 229": "OE1" <-> "OE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y ASP 285": "OD1" <-> "OD2" Residue "Y ARG 289": "NH1" <-> "NH2" Residue "Y GLU 323": "OE1" <-> "OE2" Residue "Y ASP 345": "OD1" <-> "OD2" Residue "Y PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 378": "OD1" <-> "OD2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ARG 401": "NH1" <-> "NH2" Residue "Y TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 435": "NH1" <-> "NH2" Residue "Y ARG 437": "NH1" <-> "NH2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 479": "OD1" <-> "OD2" Residue "Y PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 505": "OD1" <-> "OD2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y ASP 542": "OD1" <-> "OD2" Residue "Y ASP 548": "OD1" <-> "OD2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z ASP 91": "OD1" <-> "OD2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z ASP 136": "OD1" <-> "OD2" Residue "Z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 218": "NH1" <-> "NH2" Residue "Z GLU 219": "OE1" <-> "OE2" Residue "Z ARG 225": "NH1" <-> "NH2" Residue "Z GLU 226": "OE1" <-> "OE2" Residue "Z ARG 239": "NH1" <-> "NH2" Residue "Z TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 253": "OE1" <-> "OE2" Residue "Z GLU 296": "OE1" <-> "OE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 378": "OD1" <-> "OD2" Residue "Z ASP 381": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z GLU 428": "OE1" <-> "OE2" Residue "Z PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z ASP 548": "OD1" <-> "OD2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 552": "OE1" <-> "OE2" Residue "Z GLU 557": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 53756 Number of models: 1 Model: "" Number of chains: 37 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.77, per 1000 atoms: 0.37 Number of scatterers: 53756 At special positions: 0 Unit cell: (214.812, 134.784, 263.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 149 16.00 P 13 15.00 Mg 5 11.99 O 10174 8.00 N 9113 7.00 C 34301 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.87 Conformation dependent library (CDL) restraints added in 5.9 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 " 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 289 helices and 32 sheets defined 51.6% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.18 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 30 Processing helix chain '0' and resid 44 through 48 Processing helix chain '0' and resid 52 through 55 No H-bonds generated for 'chain '0' and resid 52 through 55' Processing helix chain '1' and resid 46 through 71 Processing helix chain '1' and resid 97 through 99 No H-bonds generated for 'chain '1' and resid 97 through 99' Processing helix chain '1' and resid 107 through 141 Processing helix chain '1' and resid 164 through 177 removed outlier: 4.165A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA 1 177 " --> pdb=" O LYS 1 173 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 201 Processing helix chain '1' and resid 207 through 223 removed outlier: 4.972A pdb=" N SER 1 211 " --> pdb=" O LYS 1 208 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU 1 223 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 242 through 270 removed outlier: 3.564A pdb=" N ARG 1 267 " --> pdb=" O LEU 1 263 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 276 removed outlier: 3.770A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 283 through 285 No H-bonds generated for 'chain '1' and resid 283 through 285' Processing helix chain '1' and resid 290 through 292 No H-bonds generated for 'chain '1' and resid 290 through 292' Processing helix chain '1' and resid 298 through 304 Processing helix chain '1' and resid 311 through 316 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: 3.717A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) Processing helix chain '1' and resid 393 through 420 removed outlier: 4.610A pdb=" N GLU 1 415 " --> pdb=" O ALA 1 411 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 426 through 431 Processing helix chain '1' and resid 436 through 443 Processing helix chain '1' and resid 447 through 459 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 514 removed outlier: 3.829A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.580A 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 593 through 605 Processing helix chain '2' and resid 8 through 18 Processing helix chain '2' and resid 26 through 39 Processing helix chain '2' and resid 45 through 56 Processing helix chain '2' and resid 63 through 76 Processing helix chain '2' and resid 81 through 93 removed outlier: 3.770A pdb=" N LEU 2 87 " --> pdb=" O THR 2 83 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA 2 88 " --> pdb=" O VAL 2 84 " (cutoff:3.500A) removed outlier: 4.845A 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: 3.704A 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 156 through 167 removed outlier: 3.674A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) Processing helix chain '2' and resid 172 through 185 Processing helix chain '2' and resid 190 through 199 removed outlier: 3.782A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS 2 198 " --> pdb=" O ASP 2 194 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER 2 199 " --> pdb=" O ALA 2 195 " (cutoff:3.500A) Processing helix chain '2' and resid 207 through 219 Processing helix chain '2' and resid 228 through 234 Processing helix chain '2' and resid 241 through 253 removed outlier: 3.523A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 259 through 275 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: 3.574A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 340 Processing helix chain '2' and resid 346 through 353 Processing helix chain '2' and resid 397 through 407 Processing helix chain '2' and resid 418 through 423 removed outlier: 4.572A pdb=" N ALA 2 423 " --> pdb=" O ASN 2 419 " (cutoff:3.500A) Processing helix chain '2' and resid 427 through 441 removed outlier: 3.652A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 79 through 85 Processing helix chain '3' and resid 98 through 100 No H-bonds generated for 'chain '3' and resid 98 through 100' Processing helix chain '3' and resid 103 through 112 removed outlier: 3.608A pdb=" N TYR 3 108 " --> pdb=" O PRO 3 104 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 128 removed outlier: 4.360A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 134 No H-bonds generated for 'chain '3' and resid 132 through 134' Processing helix chain '3' and resid 137 through 149 Processing helix chain '3' and resid 155 through 167 removed outlier: 3.784A 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: 3.968A 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: 3.720A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 240 Processing helix chain '3' and resid 246 through 250 Processing helix chain '3' and resid 254 through 271 removed outlier: 3.917A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 278 through 283 Processing helix chain '3' and resid 289 through 291 No H-bonds generated for 'chain '3' and resid 289 through 291' Processing helix chain '3' and resid 294 through 311 Processing helix chain '4' and resid 9 through 13 removed outlier: 3.685A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 9 through 13' Processing helix chain '4' and resid 20 through 34 Processing helix chain '4' and resid 48 through 69 removed outlier: 3.525A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.745A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN 4 69 " --> pdb=" O PRO 4 65 " (cutoff:3.500A) 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: 4.089A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 176 removed outlier: 3.849A pdb=" N PHE 4 165 " --> pdb=" O GLY 4 161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.673A 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 235 removed outlier: 3.640A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA 4 235 " --> pdb=" O ASP 4 231 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 258 removed outlier: 3.513A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) Processing helix chain '4' and resid 263 through 284 Processing helix chain '5' and resid 8 through 58 removed outlier: 4.810A pdb=" N LEU 5 31 " --> pdb=" O ASP 5 27 " (cutoff:3.500A) Proline residue: 5 32 - end of helix removed outlier: 3.588A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 66 No H-bonds generated for 'chain '5' and resid 64 through 66' Processing helix chain '5' and resid 73 through 80 Processing helix chain '5' and resid 88 through 105 removed outlier: 4.160A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) Processing helix chain '5' and resid 115 through 118 No H-bonds generated for 'chain '5' and resid 115 through 118' Processing helix chain '6' and resid 31 through 40 Processing helix chain '6' and resid 49 through 57 removed outlier: 4.099A pdb=" N LYS 6 52 " --> pdb=" O SER 6 49 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR 6 53 " --> pdb=" O SER 6 50 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA 6 56 " --> pdb=" O THR 6 53 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN 6 57 " --> pdb=" O ILE 6 54 " (cutoff:3.500A) Processing helix chain '6' and resid 73 through 93 Processing helix chain '6' and resid 99 through 116 removed outlier: 3.705A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 129 Processing helix chain '7' and resid 84 through 104 removed outlier: 3.746A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) Processing helix chain '7' and resid 110 through 113 Processing helix chain '7' and resid 116 through 119 No H-bonds generated for 'chain '7' and resid 116 through 119' Processing helix chain '7' and resid 124 through 144 Processing helix chain '7' and resid 147 through 164 removed outlier: 3.578A pdb=" N LEU 7 150 " --> pdb=" O PHE 7 147 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER 7 151 " --> pdb=" O ASP 7 148 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA 7 154 " --> pdb=" O SER 7 151 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER 7 155 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL 7 158 " --> pdb=" O SER 7 155 " (cutoff:3.500A) Proline residue: 7 159 - end of helix Processing helix chain '7' and resid 175 through 186 Processing helix chain '8' and resid 27 through 30 No H-bonds generated for 'chain '8' and resid 27 through 30' Processing helix chain '8' and resid 32 through 38 Processing helix chain '8' and resid 40 through 43 No H-bonds generated for 'chain '8' and resid 40 through 43' Processing helix chain '8' and resid 45 through 77 Processing helix chain '9' and resid 3 through 16 removed outlier: 3.648A pdb=" N LEU 9 7 " --> pdb=" O VAL 9 3 " (cutoff:3.500A) Processing helix chain '9' and resid 34 through 54 removed outlier: 3.950A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 83 through 94 removed outlier: 3.780A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 91 removed outlier: 4.337A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 118 removed outlier: 3.790A pdb=" N ALA A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS A 97 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 112 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.756A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 125 removed outlier: 5.771A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 110 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 119 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 120 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 121 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 124 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 125 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 91 removed outlier: 4.409A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 126 removed outlier: 3.891A pdb=" N ALA C 96 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 111 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 119 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE C 124 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU C 125 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE C 126 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 91 removed outlier: 4.220A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 125 removed outlier: 3.584A pdb=" N ALA D 96 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 105 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 91 removed outlier: 4.458A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 125 removed outlier: 3.823A pdb=" N ALA E 96 " --> pdb=" O PRO E 93 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA E 108 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLU E 111 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER E 112 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 118 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU E 125 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 91 removed outlier: 4.043A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 125 removed outlier: 3.539A pdb=" N ALA F 96 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU F 104 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE F 113 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER F 117 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 118 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU F 125 " --> pdb=" O PHE F 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 91 removed outlier: 3.985A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 125 removed outlier: 3.711A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU G 109 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU G 111 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU G 115 " --> pdb=" O SER G 112 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU G 125 " --> pdb=" O PHE G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 65 removed outlier: 3.954A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 91 removed outlier: 3.538A pdb=" N GLY H 73 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY H 77 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY H 88 " --> pdb=" O LEU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 5.583A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE H 124 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 3.539A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 126 removed outlier: 3.666A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU I 104 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU I 115 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE I 124 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE I 126 " --> pdb=" O LEU I 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 91 removed outlier: 3.905A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 125 removed outlier: 4.665A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL J 120 " --> pdb=" O PHE J 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL J 121 " --> pdb=" O SER J 117 " (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 165 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: 3.611A pdb=" N LYS M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 229 removed outlier: 4.147A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 264 removed outlier: 4.387A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA M 260 " --> pdb=" O GLY M 256 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 271 through 308 removed outlier: 3.925A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 removed outlier: 3.580A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 83 removed outlier: 4.047A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 92 removed outlier: 3.997A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 removed outlier: 4.029A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 127 removed outlier: 3.902A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 148 removed outlier: 3.767A pdb=" N LEU P 134 " --> pdb=" O LEU P 131 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 176 removed outlier: 3.525A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS P 176 " --> pdb=" O LYS P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 225 removed outlier: 3.575A pdb=" N GLU P 216 " --> pdb=" O ALA P 212 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 12 No H-bonds generated for 'chain 'Q' and resid 10 through 12' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 4.271A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 39 removed outlier: 4.329A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'R' and resid 30 through 40 removed outlier: 3.730A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 157 through 167 removed outlier: 3.831A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 195 Processing helix chain 'S' and resid 42 through 70 removed outlier: 3.652A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 78 Processing helix chain 'S' and resid 81 through 88 removed outlier: 4.466A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 116 through 127 removed outlier: 3.787A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 150 removed outlier: 3.668A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 182 Processing helix chain 'S' and resid 239 through 312 removed outlier: 3.769A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 63 Processing helix chain 'T' and resid 67 through 75 removed outlier: 4.239A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU T 74 " --> pdb=" O VAL T 70 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS T 75 " --> pdb=" O LYS T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 211 Processing helix chain 'T' and resid 231 through 246 Processing helix chain 'T' and resid 266 through 279 removed outlier: 3.520A pdb=" N ALA T 270 " --> pdb=" O ARG T 266 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN T 271 " --> pdb=" O SER T 267 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 314 Proline residue: T 303 - end of helix removed outlier: 4.168A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.776A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 352 through 362 removed outlier: 4.441A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 Processing helix chain 'T' and resid 411 through 414 No H-bonds generated for 'chain 'T' and resid 411 through 414' Processing helix chain 'T' and resid 431 through 434 removed outlier: 3.504A 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 455 removed outlier: 3.723A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL T 442 " --> pdb=" O GLY T 438 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY T 444 " --> pdb=" O LYS T 440 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR T 445 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) Processing helix chain 'T' and resid 459 through 461 No H-bonds generated for 'chain 'T' and resid 459 through 461' Processing helix chain 'T' and resid 471 through 483 Processing helix chain 'T' and resid 494 through 505 removed outlier: 3.635A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 523 through 527 Processing helix chain 'T' and resid 531 through 539 Processing helix chain 'T' and resid 544 through 555 removed outlier: 3.810A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG T 555 " --> pdb=" O LYS T 551 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 47 Processing helix chain 'U' and resid 59 through 76 removed outlier: 3.652A pdb=" N SER U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix removed outlier: 3.591A pdb=" N GLU U 72 " --> pdb=" O PRO U 68 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LYS U 75 " --> pdb=" O LYS U 71 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER U 76 " --> pdb=" O GLU U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 135 through 137 No H-bonds generated for 'chain 'U' and resid 135 through 137' Processing helix chain 'U' and resid 157 through 159 No H-bonds generated for 'chain 'U' and resid 157 through 159' Processing helix chain 'U' and resid 207 through 211 Processing helix chain 'U' and resid 231 through 246 Processing helix chain 'U' and resid 266 through 278 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 315 Proline residue: U 303 - end of helix removed outlier: 3.793A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.658A pdb=" N SER U 331 " --> pdb=" O LEU U 327 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 347 through 349 No H-bonds generated for 'chain 'U' and resid 347 through 349' Processing helix chain 'U' and resid 352 through 364 removed outlier: 4.336A pdb=" N PHE U 355 " --> pdb=" O GLY U 352 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU U 357 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG U 360 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU U 363 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 370 through 372 No H-bonds generated for 'chain 'U' and resid 370 through 372' Processing helix chain 'U' and resid 393 through 401 Processing helix chain 'U' and resid 413 through 415 No H-bonds generated for 'chain 'U' and resid 413 through 415' Processing helix chain 'U' and resid 437 through 459 removed outlier: 3.590A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU U 449 " --> pdb=" O THR U 445 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA U 457 " --> pdb=" O TYR U 453 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N PHE U 459 " --> pdb=" O GLU U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 466 through 468 No H-bonds generated for 'chain 'U' and resid 466 through 468' Processing helix chain 'U' and resid 472 through 483 removed outlier: 4.108A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 500 Processing helix chain 'U' and resid 502 through 505 No H-bonds generated for 'chain 'U' and resid 502 through 505' Processing helix chain 'U' and resid 514 through 527 removed outlier: 4.167A pdb=" N ILE U 517 " --> pdb=" O VAL U 514 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL U 518 " --> pdb=" O GLN U 515 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA U 519 " --> pdb=" O ASP U 516 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU U 521 " --> pdb=" O VAL U 518 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER U 526 " --> pdb=" O ALA U 523 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN U 527 " --> pdb=" O VAL U 524 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 539 removed outlier: 3.536A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 544 through 553 removed outlier: 3.899A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 47 No H-bonds generated for 'chain 'V' and resid 45 through 47' Processing helix chain 'V' and resid 59 through 66 Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 212 Processing helix chain 'V' and resid 231 through 246 Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 278 Processing helix chain 'V' and resid 281 through 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: 4.384A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 Processing helix chain 'V' and resid 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.362A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR V 356 " --> pdb=" O ASP V 353 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG V 364 " --> pdb=" O LEU V 361 " (cutoff:3.500A) Processing helix chain 'V' and resid 370 through 372 No H-bonds generated for 'chain 'V' and resid 370 through 372' Processing helix chain 'V' and resid 393 through 399 Processing helix chain 'V' and resid 410 through 415 Processing helix chain 'V' and resid 439 through 456 removed outlier: 3.616A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL V 456 " --> pdb=" O GLN V 452 " (cutoff:3.500A) Processing helix chain 'V' and resid 471 through 484 removed outlier: 4.035A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 505 Processing helix chain 'V' and resid 514 through 527 removed outlier: 4.002A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL V 518 " --> pdb=" O GLN V 515 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU V 521 " --> pdb=" O VAL V 518 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU V 522 " --> pdb=" O ALA V 519 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER V 526 " --> pdb=" O ALA V 523 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN V 527 " --> pdb=" O VAL V 524 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 539 Processing helix chain 'V' and resid 546 through 554 Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 167 through 170 No H-bonds generated for 'chain 'X' and resid 167 through 170' Processing helix chain 'X' and resid 189 through 200 Processing helix chain 'X' and resid 217 through 228 Processing helix chain 'X' and resid 236 through 241 removed outlier: 3.646A pdb=" N ARG X 239 " --> pdb=" O GLY X 236 " (cutoff:3.500A) removed outlier: 4.903A 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 Processing helix chain 'X' and resid 288 through 296 Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.340A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 344 No H-bonds generated for 'chain 'X' and resid 342 through 344' Processing helix chain 'X' and resid 349 through 354 removed outlier: 3.608A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) Processing helix chain 'X' and resid 366 through 371 removed outlier: 3.695A pdb=" N LEU X 371 " --> pdb=" O SER X 367 " (cutoff:3.500A) Processing helix chain 'X' and resid 394 through 420 removed outlier: 3.523A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 442 removed outlier: 3.593A pdb=" N ALA X 436 " --> pdb=" O THR X 432 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 448 through 450 No H-bonds generated for 'chain 'X' and resid 448 through 450' Processing helix chain 'X' and resid 463 through 475 Processing helix chain 'X' and resid 483 through 486 removed outlier: 3.645A pdb=" N PHE X 486 " --> pdb=" O GLU X 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 483 through 486' Processing helix chain 'X' and resid 492 through 507 removed outlier: 3.824A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 532 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 203 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 3.641A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 274 removed outlier: 5.091A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 300 Processing helix chain 'Y' and resid 314 through 322 removed outlier: 3.731A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 344 No H-bonds generated for 'chain 'Y' and resid 342 through 344' Processing helix chain 'Y' and resid 349 through 356 removed outlier: 3.774A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 393 through 411 Processing helix chain 'Y' and resid 413 through 419 removed outlier: 3.790A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 442 removed outlier: 4.615A pdb=" N VAL Y 433 " --> pdb=" O ASP Y 429 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing helix chain 'Y' and resid 463 through 475 removed outlier: 3.958A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 492 through 507 removed outlier: 3.742A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU Y 497 " --> pdb=" O LYS Y 493 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP Y 505 " --> pdb=" O LYS Y 501 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE Y 506 " --> pdb=" O MET Y 502 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA Y 507 " --> pdb=" O ALA Y 503 " (cutoff:3.500A) Processing helix chain 'Y' and resid 519 through 521 No H-bonds generated for 'chain 'Y' and resid 519 through 521' Processing helix chain 'Y' and resid 545 through 553 removed outlier: 4.175A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU Y 552 " --> pdb=" O ASP Y 548 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 150 through 152 No H-bonds generated for 'chain 'Z' and resid 150 through 152' Processing helix chain 'Z' and resid 165 through 170 Processing helix chain 'Z' and resid 191 through 200 Processing helix chain 'Z' and resid 217 through 228 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 4.705A 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: 3.587A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 288 through 298 Processing helix chain 'Z' and resid 314 through 324 removed outlier: 4.413A pdb=" N ARG Z 324 " --> pdb=" O GLY Z 320 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 357 removed outlier: 3.602A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA Z 356 " --> pdb=" O ALA Z 352 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N HIS Z 357 " --> pdb=" O THR Z 353 " (cutoff:3.500A) Processing helix chain 'Z' and resid 366 through 371 Processing helix chain 'Z' and resid 389 through 392 No H-bonds generated for 'chain 'Z' and resid 389 through 392' Processing helix chain 'Z' and resid 394 through 413 removed outlier: 3.620A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU Z 413 " --> pdb=" O ASP Z 409 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 419 No H-bonds generated for 'chain 'Z' and resid 416 through 419' Processing helix chain 'Z' and resid 422 through 424 No H-bonds generated for 'chain 'Z' and resid 422 through 424' Processing helix chain 'Z' and resid 430 through 441 removed outlier: 3.507A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 451 through 454 No H-bonds generated for 'chain 'Z' and resid 451 through 454' Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.690A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 483 through 486 Processing helix chain 'Z' and resid 492 through 499 removed outlier: 3.641A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) Processing helix chain 'Z' and resid 501 through 510 removed outlier: 3.580A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG Z 509 " --> pdb=" O ASP Z 505 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS Z 510 " --> pdb=" O ILE Z 506 " (cutoff:3.500A) Processing helix chain 'Z' and resid 528 through 532 Processing sheet with id= A, first strand: chain '2' and resid 368 through 372 removed outlier: 4.249A pdb=" N ILE 2 368 " --> pdb=" O VAL 2 379 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE 2 370 " --> pdb=" O VAL 2 377 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL 2 382 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '7' and resid 36 through 38 removed outlier: 3.706A pdb=" N ALA 7 52 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA 7 55 " --> pdb=" O ALA 7 52 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'P' and resid 151 through 153 removed outlier: 7.078A pdb=" N LYS P 183 " --> pdb=" O VAL P 152 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'P' and resid 188 through 190 removed outlier: 6.587A pdb=" N VAL P 156 " --> pdb=" O LYS P 189 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE P 198 " --> pdb=" O MET P 209 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'Q' and resid 45 through 49 Processing sheet with id= F, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.987A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 96 through 100 removed outlier: 3.620A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY R 114 " --> pdb=" O VAL R 129 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'S' and resid 203 through 211 removed outlier: 5.205A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'T' and resid 84 through 86 removed outlier: 3.991A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY T 128 " --> pdb=" O LEU T 120 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR T 98 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL T 87 " --> pdb=" O TYR T 98 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= K, first strand: chain 'T' and resid 404 through 408 removed outlier: 3.549A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 376 through 381 Processing sheet with id= M, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.574A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'U' and resid 109 through 111 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: 8.733A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.989A 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 84 through 86 removed outlier: 6.457A pdb=" N GLY V 128 " --> pdb=" O LEU V 120 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU V 122 " --> pdb=" O HIS V 126 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N HIS V 126 " --> pdb=" O LEU V 122 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR V 98 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL V 87 " --> pdb=" O TYR V 98 " (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: 8.740A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.684A 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 38 through 44 removed outlier: 6.297A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 158 through 160 removed outlier: 4.773A pdb=" N GLU X 158 " --> pdb=" O ARG X 175 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.629A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE X 207 " --> pdb=" O LEU X 281 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHE X 283 " --> pdb=" O PHE X 207 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL X 209 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ASP X 285 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 7.249A 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 39 through 44 removed outlier: 6.283A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id= AB, first strand: chain 'Y' and resid 244 through 250 removed outlier: 6.624A pdb=" N SER Y 208 " --> pdb=" O THR Y 245 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL Y 247 " --> pdb=" O SER Y 208 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE Y 210 " --> pdb=" O VAL Y 247 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLY Y 249 " --> pdb=" O PHE Y 210 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLY Y 212 " --> pdb=" O GLY Y 249 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N VAL Y 209 " --> pdb=" O ASP Y 279 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU Y 281 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ALA Y 211 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE Y 283 " --> pdb=" O ALA Y 211 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL Y 213 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 213 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU Y 215 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER Y 332 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU Y 282 " --> pdb=" O SER Y 332 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR Y 334 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL Y 284 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 284 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLY Y 180 " --> pdb=" O ASP Y 359 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR Y 361 " --> pdb=" O GLY Y 180 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N PHE Y 182 " --> pdb=" O THR Y 361 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL Y 363 " --> pdb=" O PHE Y 182 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Z' and resid 37 through 39 removed outlier: 6.480A pdb=" N ARG Z 86 " --> pdb=" O ALA Z 77 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N HIS Z 79 " --> pdb=" O THR Z 84 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR Z 84 " --> pdb=" O HIS Z 79 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG Z 51 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL Z 40 " --> pdb=" O ARG Z 51 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.558A pdb=" N ASP Z 139 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 360 through 363 removed outlier: 7.216A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLY Z 183 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL Z 339 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE Z 207 " --> pdb=" O LEU Z 281 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N PHE Z 283 " --> pdb=" O PHE Z 207 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL Z 209 " --> pdb=" O PHE Z 283 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASP Z 285 " --> pdb=" O VAL Z 209 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA Z 211 " --> pdb=" O ASP Z 285 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Z' and resid 559 through 561 2424 hydrogen bonds defined for protein. 6348 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.09 Time building geometry restraints manager: 17.31 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: 13556 1.33 - 1.45: 9967 1.45 - 1.57: 30896 1.57 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54694 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.81e+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 4.70e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.54e+01 bond pdb=" C5 ATP V1001 " pdb=" N7 ATP V1001 " ideal model delta sigma weight residual 1.387 1.327 0.060 1.00e-02 1.00e+04 3.65e+01 bond pdb=" C5 ATP T1001 " pdb=" N7 ATP T1001 " ideal model delta sigma weight residual 1.387 1.331 0.056 1.00e-02 1.00e+04 3.19e+01 ... (remaining 54689 not shown) Histogram of bond angle deviations from ideal: 94.01 - 102.40: 212 102.40 - 110.80: 18566 110.80 - 119.19: 27614 119.19 - 127.59: 27366 127.59 - 135.98: 414 Bond angle restraints: 74172 Sorted by residual: angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 122.18 17.69 1.00e+00 1.00e+00 3.13e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 122.51 17.36 1.00e+00 1.00e+00 3.01e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 124.30 15.57 1.00e+00 1.00e+00 2.42e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.81 13.02 1.00e+00 1.00e+00 1.69e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 125.05 11.78 1.00e+00 1.00e+00 1.39e+02 ... (remaining 74167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.25: 31899 30.25 - 60.50: 961 60.50 - 90.75: 73 90.75 - 121.00: 1 121.00 - 151.25: 3 Dihedral angle restraints: 32937 sinusoidal: 12576 harmonic: 20361 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -122.82 -57.18 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual 180.00 -133.04 -46.96 0 5.00e+00 4.00e-02 8.82e+01 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual 180.00 -134.40 -45.60 0 5.00e+00 4.00e-02 8.32e+01 ... (remaining 32934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 6917 0.075 - 0.151: 1597 0.151 - 0.226: 150 0.226 - 0.301: 23 0.301 - 0.377: 3 Chirality restraints: 8690 Sorted by residual: chirality pdb=" CB VAL V 180 " pdb=" CA VAL V 180 " pdb=" CG1 VAL V 180 " pdb=" CG2 VAL V 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CB ILE Y 524 " pdb=" CA ILE Y 524 " pdb=" CG1 ILE Y 524 " pdb=" CG2 ILE Y 524 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CG LEU U 202 " pdb=" CB LEU U 202 " pdb=" CD1 LEU U 202 " pdb=" CD2 LEU U 202 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 8687 not shown) Planarity restraints: 9512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.22e-02 3.87e+01 pdb=" C ALA Z 503 " -0.108 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA X 503 " -0.030 2.00e-02 2.50e+03 5.78e-02 3.34e+01 pdb=" C ALA X 503 " 0.100 2.00e-02 2.50e+03 pdb=" O ALA X 503 " -0.037 2.00e-02 2.50e+03 pdb=" N LYS X 504 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL Z 341 " -0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO Z 342 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO Z 342 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO Z 342 " -0.047 5.00e-02 4.00e+02 ... (remaining 9509 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1684 2.69 - 3.24: 51991 3.24 - 3.80: 89391 3.80 - 4.35: 119536 4.35 - 4.90: 197225 Nonbonded interactions: 459827 Sorted by model distance: nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 2.140 2.170 nonbonded pdb=" OH TYR 9 90 " pdb=" CE LYS 9 94 " model vdw 2.168 3.440 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.197 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.218 2.170 nonbonded pdb=" OH TYR 5 62 " pdb=" O PHE 6 146 " model vdw 2.241 2.440 ... (remaining 459822 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 36 through 556) selection = chain 'Y' selection = (chain 'Z' and resid 36 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 25.660 Check model and map are aligned: 0.600 Set scattering table: 0.360 Process input model: 109.970 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.300 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: 0.020 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.011 0.121 54694 Z= 0.746 Angle : 1.022 17.687 74172 Z= 0.576 Chirality : 0.062 0.377 8690 Planarity : 0.008 0.086 9512 Dihedral : 14.396 151.251 19849 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.06 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.08), residues: 7039 helix: -2.90 (0.06), residues: 3824 sheet: -1.50 (0.20), residues: 606 loop : -2.11 (0.10), residues: 2609 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 903 time to evaluate : 4.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 917 average time/residue: 0.5652 time to fit residues: 845.0434 Evaluate side-chains 614 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 604 time to evaluate : 4.461 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3683 time to fit residues: 13.1235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 8.9990 chunk 529 optimal weight: 6.9990 chunk 293 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 356 optimal weight: 0.4980 chunk 282 optimal weight: 2.9990 chunk 547 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 332 optimal weight: 2.9990 chunk 407 optimal weight: 0.8980 chunk 633 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 65 GLN 1 257 HIS 1 298 GLN 1 316 ASN 1 365 GLN 1 482 ASN 1 587 ASN 1 590 HIS 1 606 ASN 2 68 ASN 2 243 GLN 3 87 ASN 3 164 ASN 3 206 ASN 3 229 ASN 4 52 GLN 4 135 ASN 5 29 GLN 5 107 ASN 5 117 GLN 6 40 ASN 6 74 GLN 7 98 ASN 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 35 GLN A 94 ASN B 94 ASN E 94 ASN G 92 ASN I 98 GLN M 108 ASN M 163 ASN P 52 GLN P 220 ASN R 38 ASN R 66 HIS R 73 ASN R 83 GLN R 137 HIS R 139 ASN S 52 ASN S 98 ASN S 174 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 219 GLN S 262 ASN T 134 ASN T 241 HIS T 435 GLN T 441 GLN T 497 GLN U 123 GLN U 386 GLN U 422 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 121 ASN V 134 ASN V 139 HIS V 152 ASN V 196 GLN V 241 HIS V 242 GLN V 244 ASN V 386 GLN V 435 GLN V 486 GLN V 497 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 529 ASN V 549 HIS X 83 ASN X 241 ASN X 390 ASN X 398 ASN X 414 GLN Y 199 ASN Y 278 GLN Y 294 ASN Y 322 GLN Y 337 GLN Y 388 ASN Y 398 ASN Y 404 GLN Y 414 GLN Z 42 GLN Z 199 ASN ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 337 GLN Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 54694 Z= 0.215 Angle : 0.572 10.768 74172 Z= 0.302 Chirality : 0.042 0.230 8690 Planarity : 0.005 0.061 9512 Dihedral : 6.147 130.843 7578 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.76 % Favored : 96.11 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.09), residues: 7039 helix: -1.21 (0.08), residues: 3799 sheet: -1.14 (0.21), residues: 584 loop : -1.57 (0.11), residues: 2656 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 706 time to evaluate : 5.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 53 residues processed: 763 average time/residue: 0.5279 time to fit residues: 675.9893 Evaluate side-chains 635 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 582 time to evaluate : 4.500 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.4027 time to fit residues: 46.1388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 527 optimal weight: 1.9990 chunk 431 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 635 optimal weight: 6.9990 chunk 685 optimal weight: 0.7980 chunk 565 optimal weight: 0.3980 chunk 629 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 509 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 380 GLN 5 107 ASN 7 170 HIS 8 26 HIS 9 35 GLN A 87 ASN G 94 ASN H 98 GLN J 98 GLN R 85 GLN R 154 GLN S 96 ASN S 98 ASN T 179 ASN T 488 GLN U 497 GLN V 549 HIS X 414 GLN Z 157 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 54694 Z= 0.250 Angle : 0.558 10.955 74172 Z= 0.290 Chirality : 0.043 0.188 8690 Planarity : 0.004 0.052 9512 Dihedral : 5.605 101.205 7578 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.87 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.10), residues: 7039 helix: -0.51 (0.08), residues: 3789 sheet: -1.01 (0.21), residues: 612 loop : -1.19 (0.12), residues: 2638 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 650 time to evaluate : 4.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 45 residues processed: 718 average time/residue: 0.5173 time to fit residues: 629.0709 Evaluate side-chains 631 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 586 time to evaluate : 4.499 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.3912 time to fit residues: 39.3474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 2.9990 chunk 477 optimal weight: 5.9990 chunk 329 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 303 optimal weight: 0.0770 chunk 426 optimal weight: 0.8980 chunk 637 optimal weight: 6.9990 chunk 674 optimal weight: 6.9990 chunk 332 optimal weight: 0.0770 chunk 603 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 overall best weight: 0.9498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 68 ASN ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 52 GLN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 35 GLN C 94 ASN H 98 GLN I 98 GLN P 52 GLN P 83 GLN R 85 GLN S 98 ASN T 386 GLN U 319 HIS U 358 HIS ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 549 HIS X 414 GLN Z 68 HIS Z 144 HIS Z 440 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 54694 Z= 0.176 Angle : 0.520 10.118 74172 Z= 0.268 Chirality : 0.041 0.192 8690 Planarity : 0.004 0.047 9512 Dihedral : 5.193 77.545 7578 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.21 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.10), residues: 7039 helix: -0.10 (0.09), residues: 3810 sheet: -0.80 (0.21), residues: 589 loop : -0.95 (0.12), residues: 2640 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 675 time to evaluate : 4.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 40 residues processed: 736 average time/residue: 0.5235 time to fit residues: 653.3994 Evaluate side-chains 643 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 603 time to evaluate : 4.443 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3916 time to fit residues: 35.8514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 0.8980 chunk 382 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 502 optimal weight: 3.9990 chunk 278 optimal weight: 10.0000 chunk 575 optimal weight: 0.8980 chunk 466 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 344 optimal weight: 0.0980 chunk 605 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 111 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN F 92 ASN I 98 GLN P 52 GLN P 83 GLN Q 46 HIS R 85 GLN S 98 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 54694 Z= 0.162 Angle : 0.511 10.669 74172 Z= 0.262 Chirality : 0.041 0.237 8690 Planarity : 0.004 0.046 9512 Dihedral : 4.975 72.309 7578 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.71 % Favored : 96.16 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.10), residues: 7039 helix: 0.18 (0.09), residues: 3735 sheet: -0.67 (0.21), residues: 589 loop : -0.77 (0.12), residues: 2715 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 655 time to evaluate : 4.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 29 residues processed: 693 average time/residue: 0.5214 time to fit residues: 608.2874 Evaluate side-chains 617 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 588 time to evaluate : 4.410 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3772 time to fit residues: 26.8786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 226 optimal weight: 5.9990 chunk 607 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 396 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 675 optimal weight: 3.9990 chunk 560 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 354 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 111 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN F 92 ASN I 98 GLN P 83 GLN R 85 GLN R 154 GLN S 96 ASN S 98 ASN T 134 ASN T 497 GLN X 414 GLN Y 414 GLN Z 241 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 54694 Z= 0.282 Angle : 0.557 11.491 74172 Z= 0.285 Chirality : 0.043 0.201 8690 Planarity : 0.004 0.047 9512 Dihedral : 5.098 76.331 7578 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.06 % Favored : 95.82 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.10), residues: 7039 helix: 0.21 (0.09), residues: 3742 sheet: -0.75 (0.21), residues: 622 loop : -0.71 (0.12), residues: 2675 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 601 time to evaluate : 5.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 43 residues processed: 656 average time/residue: 0.5302 time to fit residues: 589.2874 Evaluate side-chains 616 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 573 time to evaluate : 4.520 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.3980 time to fit residues: 38.2907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 384 optimal weight: 0.0870 chunk 493 optimal weight: 1.9990 chunk 382 optimal weight: 0.9990 chunk 568 optimal weight: 0.2980 chunk 377 optimal weight: 3.9990 chunk 672 optimal weight: 0.9990 chunk 421 optimal weight: 3.9990 chunk 410 optimal weight: 0.6980 chunk 310 optimal weight: 2.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 35 GLN C 94 ASN P 52 GLN R 85 GLN R 154 GLN S 98 ASN T 179 ASN T 497 GLN V 515 GLN V 549 HIS X 414 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 54694 Z= 0.150 Angle : 0.510 11.716 74172 Z= 0.259 Chirality : 0.040 0.220 8690 Planarity : 0.004 0.045 9512 Dihedral : 4.833 71.305 7578 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.52 % Favored : 96.36 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.10), residues: 7039 helix: 0.46 (0.09), residues: 3738 sheet: -0.66 (0.21), residues: 608 loop : -0.62 (0.12), residues: 2693 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 642 time to evaluate : 4.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 23 residues processed: 667 average time/residue: 0.5214 time to fit residues: 587.8152 Evaluate side-chains 611 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 588 time to evaluate : 4.580 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3932 time to fit residues: 23.0589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 1.9990 chunk 268 optimal weight: 0.6980 chunk 401 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 427 optimal weight: 2.9990 chunk 458 optimal weight: 0.9980 chunk 332 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 528 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 409 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 35 GLN C 94 ASN P 52 GLN R 85 GLN R 181 ASN S 98 ASN T 497 GLN V 549 HIS X 123 ASN X 414 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 54694 Z= 0.187 Angle : 0.521 12.093 74172 Z= 0.264 Chirality : 0.041 0.188 8690 Planarity : 0.004 0.044 9512 Dihedral : 4.789 68.975 7578 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.21 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.10), residues: 7039 helix: 0.52 (0.09), residues: 3753 sheet: -0.67 (0.21), residues: 622 loop : -0.59 (0.12), residues: 2664 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 609 time to evaluate : 4.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 24 residues processed: 626 average time/residue: 0.5343 time to fit residues: 567.7571 Evaluate side-chains 601 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 577 time to evaluate : 4.492 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4112 time to fit residues: 24.7029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 2.9990 chunk 644 optimal weight: 0.5980 chunk 588 optimal weight: 5.9990 chunk 626 optimal weight: 0.0170 chunk 377 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 492 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 566 optimal weight: 2.9990 chunk 592 optimal weight: 3.9990 chunk 624 optimal weight: 0.6980 overall best weight: 1.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN R 85 GLN R 154 GLN S 98 ASN T 134 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 497 GLN V 549 HIS X 414 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 54694 Z= 0.210 Angle : 0.532 12.121 74172 Z= 0.269 Chirality : 0.042 0.186 8690 Planarity : 0.004 0.044 9512 Dihedral : 4.809 69.631 7578 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.75 % Favored : 96.14 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.10), residues: 7039 helix: 0.56 (0.09), residues: 3737 sheet: -0.70 (0.21), residues: 634 loop : -0.54 (0.12), residues: 2668 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 595 time to evaluate : 4.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 607 average time/residue: 0.5554 time to fit residues: 572.2930 Evaluate side-chains 577 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 568 time to evaluate : 4.522 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4177 time to fit residues: 13.1745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 0.6980 chunk 662 optimal weight: 4.9990 chunk 404 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 460 optimal weight: 2.9990 chunk 695 optimal weight: 0.8980 chunk 640 optimal weight: 0.0970 chunk 553 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 427 optimal weight: 3.9990 chunk 339 optimal weight: 8.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN P 52 GLN R 83 GLN R 85 GLN R 154 GLN S 98 ASN V 549 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 54694 Z= 0.218 Angle : 0.536 12.166 74172 Z= 0.272 Chirality : 0.042 0.186 8690 Planarity : 0.004 0.044 9512 Dihedral : 4.839 70.525 7578 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.84 % Favored : 96.05 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.10), residues: 7039 helix: 0.56 (0.09), residues: 3747 sheet: -0.61 (0.21), residues: 625 loop : -0.50 (0.12), residues: 2667 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 586 time to evaluate : 4.628 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 595 average time/residue: 0.5513 time to fit residues: 553.4553 Evaluate side-chains 575 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 570 time to evaluate : 4.557 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3961 time to fit residues: 9.9825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 1.9990 chunk 589 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 510 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 554 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 569 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 380 GLN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 35 GLN C 94 ASN C 98 GLN F 92 ASN P 52 GLN R 83 GLN R 154 GLN S 98 ASN V 549 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.102876 restraints weight = 79012.839| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.58 r_work: 0.3010 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 54694 Z= 0.237 Angle : 0.546 13.027 74172 Z= 0.277 Chirality : 0.042 0.201 8690 Planarity : 0.004 0.045 9512 Dihedral : 4.881 71.866 7578 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.82 % Favored : 96.06 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.10), residues: 7039 helix: 0.57 (0.09), residues: 3746 sheet: -0.58 (0.21), residues: 616 loop : -0.51 (0.12), residues: 2677 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11380.23 seconds wall clock time: 201 minutes 39.89 seconds (12099.89 seconds total)