Starting phenix.real_space_refine on Thu Dec 7 19:11:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re9_4846/12_2023/6re9_4846_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re9_4846/12_2023/6re9_4846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re9_4846/12_2023/6re9_4846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re9_4846/12_2023/6re9_4846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re9_4846/12_2023/6re9_4846_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re9_4846/12_2023/6re9_4846_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34282 2.51 5 N 9107 2.21 5 O 10163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 96": "OD1" <-> "OD2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 GLU 165": "OE1" <-> "OE2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 GLU 198": "OE1" <-> "OE2" Residue "1 GLU 223": "OE1" <-> "OE2" Residue "1 GLU 229": "OE1" <-> "OE2" Residue "1 GLU 235": "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 332": "OE1" <-> "OE2" Residue "1 GLU 334": "OE1" <-> "OE2" Residue "1 GLU 339": "OE1" <-> "OE2" Residue "1 GLU 343": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 GLU 385": "OE1" <-> "OE2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 GLU 409": "OE1" <-> "OE2" Residue "1 TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 452": "OE1" <-> "OE2" Residue "1 GLU 495": "OE1" <-> "OE2" Residue "1 ASP 508": "OD1" <-> "OD2" Residue "1 GLU 513": "OE1" <-> "OE2" Residue "1 GLU 517": "OE1" <-> "OE2" Residue "1 ASP 549": "OD1" <-> "OD2" Residue "1 GLU 565": "OE1" <-> "OE2" Residue "1 ASP 568": "OD1" <-> "OD2" Residue "1 GLU 586": "OE1" <-> "OE2" Residue "1 ASP 601": "OD1" <-> "OD2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 86": "OE1" <-> "OE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 ASP 194": "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 GLU 246": "OE1" <-> "OE2" Residue "2 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 281": "OE1" <-> "OE2" Residue "2 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 316": "OD1" <-> "OD2" Residue "2 GLU 326": "OE1" <-> "OE2" Residue "2 PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 346": "NH1" <-> "NH2" Residue "2 TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 126": "OE1" <-> "OE2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 ASP 154": "OD1" <-> "OD2" Residue "3 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 173": "OE1" <-> "OE2" Residue "3 GLU 175": "OE1" <-> "OE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 197": "OD1" <-> "OD2" Residue "3 ARG 213": "NH1" <-> "NH2" Residue "3 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 233": "NH1" <-> "NH2" Residue "3 ARG 242": "NH1" <-> "NH2" Residue "3 ARG 257": "NH1" <-> "NH2" Residue "3 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 291": "OE1" <-> "OE2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 45": "OD1" <-> "OD2" Residue "4 ARG 84": "NH1" <-> "NH2" Residue "4 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 156": "OD1" <-> "OD2" Residue "4 ARG 176": "NH1" <-> "NH2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 193": "OE1" <-> "OE2" Residue "4 GLU 202": "OE1" <-> "OE2" Residue "4 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 214": "OD1" <-> "OD2" Residue "4 GLU 218": "OE1" <-> "OE2" Residue "4 ASP 231": "OD1" <-> "OD2" Residue "4 ARG 232": "NH1" <-> "NH2" Residue "4 GLU 244": "OE1" <-> "OE2" Residue "4 ARG 255": "NH1" <-> "NH2" Residue "4 GLU 266": "OE1" <-> "OE2" Residue "4 TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 GLU 90": "OE1" <-> "OE2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "5 PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 91": "OD1" <-> "OD2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 47": "OE1" <-> "OE2" Residue "7 GLU 78": "OE1" <-> "OE2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 GLU 99": "OE1" <-> "OE2" Residue "7 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 136": "OE1" <-> "OE2" 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 ASP 10": "OD1" <-> "OD2" Residue "8 ARG 13": "NH1" <-> "NH2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "8 TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 12": "OE1" <-> "OE2" Residue "9 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 22": "OE1" <-> "OE2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 40": "NH1" <-> "NH2" Residue "9 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 74": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "J PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M GLU 124": "OE1" <-> "OE2" Residue "M ARG 145": "NH1" <-> "NH2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 221": "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 GLU 64": "OE1" <-> "OE2" Residue "P GLU 79": "OE1" <-> "OE2" Residue "P ASP 93": "OD1" <-> "OD2" Residue "P GLU 116": "OE1" <-> "OE2" Residue "P PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 163": "OD1" <-> "OD2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 204": "OD1" <-> "OD2" 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 ASP 25": "OD1" <-> "OD2" Residue "Q GLU 33": "OE1" <-> "OE2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 54": "OD1" <-> "OD2" Residue "Q TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 62": "OE1" <-> "OE2" Residue "R PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "R GLU 148": "OE1" <-> "OE2" Residue "R ASP 156": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S GLU 154": "OE1" <-> "OE2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 181": "OE1" <-> "OE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 214": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S ASP 245": "OD1" <-> "OD2" Residue "S GLU 275": "OE1" <-> "OE2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 303": "OE1" <-> "OE2" Residue "T GLU 47": "OE1" <-> "OE2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 112": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" 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 ASP 237": "OD1" <-> "OD2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T ASP 353": "OD1" <-> "OD2" Residue "T GLU 371": "OE1" <-> "OE2" Residue "T GLU 384": "OE1" <-> "OE2" Residue "T ASP 389": "OD1" <-> "OD2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 449": "OE1" <-> "OE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T GLU 455": "OE1" <-> "OE2" Residue "T PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 467": "OD1" <-> "OD2" Residue "T GLU 475": "OE1" <-> "OE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 522": "OE1" <-> "OE2" Residue "T ASP 547": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 41": "OD1" <-> "OD2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 92": "OD1" <-> "OD2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 112": "OD1" <-> "OD2" Residue "U ASP 142": "OD1" <-> "OD2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U GLU 200": "OE1" <-> "OE2" Residue "U PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ASP 237": "OD1" <-> "OD2" 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 GLU 411": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 467": "OD1" <-> "OD2" 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 PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 547": "OD1" <-> "OD2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 72": "OE1" <-> "OE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V GLU 186": "OE1" <-> "OE2" Residue "V ASP 210": "OD1" <-> "OD2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V ASP 226": "OD1" <-> "OD2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 347": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V GLU 482": "OE1" <-> "OE2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X ASP 53": "OD1" <-> "OD2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X GLU 195": "OE1" <-> "OE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X ASP 222": "OD1" <-> "OD2" Residue "X GLU 238": "OE1" <-> "OE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X ASP 285": "OD1" <-> "OD2" Residue "X ASP 317": "OD1" <-> "OD2" Residue "X ASP 345": "OD1" <-> "OD2" Residue "X ASP 348": "OD1" <-> "OD2" Residue "X PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 370": "OE1" <-> "OE2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X ASP 409": "OD1" <-> "OD2" Residue "X TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 435": "NH1" <-> "NH2" Residue "X ARG 437": "NH1" <-> "NH2" Residue "X PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 500": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 511": "OE1" <-> "OE2" Residue "X GLU 519": "OE1" <-> "OE2" Residue "X GLU 520": "OE1" <-> "OE2" Residue "X PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 552": "OE1" <-> "OE2" Residue "X GLU 557": "OE1" <-> "OE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y ASP 82": "OD1" <-> "OD2" Residue "Y ASP 94": "OD1" <-> "OD2" Residue "Y ASP 104": "OD1" <-> "OD2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 168": "OD1" <-> "OD2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 218": "NH1" <-> "NH2" Residue "Y ARG 225": "NH1" <-> "NH2" Residue "Y ARG 239": "NH1" <-> "NH2" Residue "Y TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 296": "OE1" <-> "OE2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 401": "NH1" <-> "NH2" Residue "Y ASP 429": "OD1" <-> "OD2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 479": "OD1" <-> "OD2" Residue "Y GLU 494": "OE1" <-> "OE2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y GLU 540": "OE1" <-> "OE2" Residue "Y GLU 541": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 552": "OE1" <-> "OE2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ASP 82": "OD1" <-> "OD2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 115": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z ASP 136": "OD1" <-> "OD2" Residue "Z ARG 145": "NH1" <-> "NH2" Residue "Z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 152": "OE1" <-> "OE2" Residue "Z TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 195": "OE1" <-> "OE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z ASP 279": "OD1" <-> "OD2" Residue "Z GLU 296": "OE1" <-> "OE2" Residue "Z TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 317": "OD1" <-> "OD2" Residue "Z GLU 323": "OE1" <-> "OE2" Residue "Z ASP 344": "OD1" <-> "OD2" Residue "Z ARG 366": "NH1" <-> "NH2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z ASP 415": "OD1" <-> "OD2" Residue "Z GLU 427": "OE1" <-> "OE2" Residue "Z ASP 429": "OD1" <-> "OD2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 513": "OD1" <-> "OD2" Residue "Z GLU 520": "OE1" <-> "OE2" Residue "Z ASP 523": "OD1" <-> "OD2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 53720 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: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3961 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "Y" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3952 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 497} Chain: "Z" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.94, per 1000 atoms: 0.39 Number of scatterers: 53720 At special positions: 0 Unit cell: (214.812, 135.837, 262.197, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 149 16.00 P 13 15.00 Mg 5 11.99 O 10163 8.00 N 9107 7.00 C 34282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.38 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 284 helices and 31 sheets defined 51.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.69 Creating SS restraints... Processing helix chain '0' and resid 4 through 7 No H-bonds generated for 'chain '0' and resid 4 through 7' Processing helix chain '0' and resid 18 through 29 Processing helix chain '0' and resid 44 through 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 107 through 141 removed outlier: 3.547A pdb=" N GLU 1 136 " --> pdb=" O GLY 1 132 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) Processing helix chain '1' and resid 164 through 178 removed outlier: 3.911A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA 1 177 " --> pdb=" O LYS 1 173 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU 1 178 " --> pdb=" O TYR 1 174 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 203 removed outlier: 3.615A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE 1 200 " --> pdb=" O ALA 1 196 " (cutoff:3.500A) Processing helix chain '1' and resid 210 through 223 Processing helix chain '1' and resid 242 through 270 removed outlier: 3.859A pdb=" N ARG 1 267 " --> pdb=" O LEU 1 263 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 276 removed outlier: 3.729A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 283 through 285 No H-bonds generated for 'chain '1' and resid 283 through 285' Processing helix chain '1' and resid 298 through 304 Processing helix chain '1' and resid 311 through 316 Processing helix chain '1' and resid 331 through 333 No H-bonds generated for 'chain '1' and resid 331 through 333' Processing helix chain '1' and resid 339 through 350 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: 3.883A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) Processing helix chain '1' and resid 393 through 420 removed outlier: 4.420A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 4.761A 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 444 Processing helix chain '1' and resid 447 through 459 Processing helix chain '1' and resid 464 through 477 Processing helix chain '1' and resid 480 through 482 No H-bonds generated for 'chain '1' and resid 480 through 482' Processing helix chain '1' and resid 486 through 489 No H-bonds generated for 'chain '1' and resid 486 through 489' Processing helix chain '1' and resid 491 through 515 removed outlier: 4.074A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) Processing helix chain '1' and resid 519 through 535 Processing helix chain '1' and resid 542 through 548 Processing helix chain '1' and resid 550 through 561 Processing helix chain '1' and resid 567 through 573 Processing helix chain '1' and resid 577 through 587 Processing helix chain '1' and resid 589 through 605 removed outlier: 3.567A pdb=" N PHE 1 592 " --> pdb=" O SER 1 589 " (cutoff:3.500A) Proline residue: 1 594 - end of helix removed outlier: 3.559A pdb=" N ARG 1 599 " --> pdb=" O ILE 1 596 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA 1 603 " --> pdb=" O ARG 1 600 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 19 Processing helix chain '2' and resid 26 through 37 Processing helix chain '2' and resid 45 through 57 Processing helix chain '2' and resid 63 through 75 Processing helix chain '2' and resid 81 through 93 removed outlier: 4.080A pdb=" N ALA 2 88 " --> pdb=" O VAL 2 84 " (cutoff:3.500A) removed outlier: 5.105A 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 95 through 97 No H-bonds generated for 'chain '2' and resid 95 through 97' Processing helix chain '2' and resid 100 through 112 Processing helix chain '2' and resid 118 through 130 Processing helix chain '2' and resid 137 through 148 Processing helix chain '2' and resid 156 through 167 removed outlier: 3.800A 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: 3.616A pdb=" N LYS 2 198 " --> pdb=" O ASP 2 194 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER 2 199 " --> pdb=" O ALA 2 195 " (cutoff:3.500A) Processing helix chain '2' and resid 207 through 220 Processing helix chain '2' and resid 229 through 234 Processing helix chain '2' and resid 241 through 253 removed outlier: 3.810A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 259 through 266 Processing helix chain '2' and resid 270 through 275 Processing helix chain '2' and resid 282 through 294 Processing helix chain '2' and resid 301 through 320 removed outlier: 4.029A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) Processing helix chain '2' and resid 327 through 340 Processing helix chain '2' and resid 346 through 355 Processing helix chain '2' and resid 397 through 409 removed outlier: 3.560A pdb=" N ALA 2 408 " --> pdb=" O LYS 2 404 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN 2 409 " --> pdb=" O VAL 2 405 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 423 removed outlier: 3.787A pdb=" N GLU 2 422 " --> pdb=" O ALA 2 418 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA 2 423 " --> pdb=" O ASN 2 419 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 418 through 423' Processing helix chain '2' and resid 427 through 441 removed outlier: 4.158A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 88 Processing helix chain '3' and resid 92 through 95 No H-bonds generated for 'chain '3' and resid 92 through 95' Processing helix chain '3' and resid 103 through 112 Processing helix chain '3' and resid 118 through 127 removed outlier: 3.888A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU 3 126 " --> pdb=" O VAL 3 122 " (cutoff:3.500A) Processing helix chain '3' and resid 129 through 134 removed outlier: 4.045A pdb=" N VAL 3 132 " --> pdb=" O LYS 3 129 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ALA 3 133 " --> pdb=" O PRO 3 130 " (cutoff:3.500A) Processing helix chain '3' and resid 137 through 149 Processing helix chain '3' and resid 155 through 167 removed outlier: 3.766A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 169 through 171 No H-bonds generated for 'chain '3' and resid 169 through 171' Processing helix chain '3' and resid 174 through 186 removed outlier: 4.023A 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: 3.983A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 243 removed outlier: 3.934A pdb=" N ARG 3 242 " --> pdb=" O ALA 3 238 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY 3 243 " --> pdb=" O THR 3 239 " (cutoff:3.500A) Processing helix chain '3' and resid 246 through 250 Processing helix chain '3' and resid 255 through 271 Processing helix chain '3' and resid 276 through 286 removed outlier: 4.041A pdb=" N GLU 3 279 " --> pdb=" O GLU 3 276 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA 3 280 " --> pdb=" O SER 3 277 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA 3 284 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU 3 286 " --> pdb=" O GLY 3 283 " (cutoff:3.500A) Processing helix chain '3' and resid 294 through 311 removed outlier: 3.504A pdb=" N VAL 3 303 " --> pdb=" O GLU 3 299 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 13 No H-bonds generated for 'chain '4' and resid 10 through 13' Processing helix chain '4' and resid 21 through 34 Processing helix chain '4' and resid 48 through 69 removed outlier: 3.743A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.900A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) removed outlier: 3.572A 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: 3.721A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 175 removed outlier: 3.970A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 180 through 188 Processing helix chain '4' and resid 193 through 233 removed outlier: 4.321A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 258 Processing helix chain '4' and resid 263 through 284 Processing helix chain '4' and resid 286 through 288 No H-bonds generated for 'chain '4' and resid 286 through 288' Processing helix chain '5' and resid 8 through 58 removed outlier: 5.140A pdb=" N LEU 5 31 " --> pdb=" O ASP 5 27 " (cutoff:3.500A) Proline residue: 5 32 - end of helix removed outlier: 3.962A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 67 No H-bonds generated for 'chain '5' and resid 64 through 67' Processing helix chain '5' and resid 73 through 80 Processing helix chain '5' and resid 88 through 105 removed outlier: 4.291A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) Processing helix chain '6' and resid 31 through 40 Processing helix chain '6' and resid 52 through 57 Processing helix chain '6' and resid 73 through 92 Processing helix chain '6' and resid 99 through 119 removed outlier: 3.990A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 130 Processing helix chain '6' and resid 134 through 137 No H-bonds generated for 'chain '6' and resid 134 through 137' Processing helix chain '7' and resid 63 through 66 No H-bonds generated for 'chain '7' and resid 63 through 66' Processing helix chain '7' and resid 84 through 101 Processing helix chain '7' and resid 111 through 113 No H-bonds generated for 'chain '7' and resid 111 through 113' Processing helix chain '7' and resid 116 through 119 No H-bonds generated for 'chain '7' and resid 116 through 119' Processing helix chain '7' and resid 124 through 144 Processing helix chain '7' and resid 147 through 164 removed outlier: 3.597A pdb=" N LEU 7 150 " --> pdb=" O PHE 7 147 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER 7 151 " --> pdb=" O ASP 7 148 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER 7 155 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) removed outlier: 4.651A 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 77 removed outlier: 6.820A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) Processing helix chain '9' and resid 6 through 16 Processing helix chain '9' and resid 33 through 54 removed outlier: 4.126A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 77 through 79 No H-bonds generated for 'chain '9' and resid 77 through 79' Processing helix chain '9' and resid 83 through 93 removed outlier: 3.594A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 91 removed outlier: 3.580A pdb=" N ALA A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 126 removed outlier: 3.728A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 66 Processing helix chain 'B' and resid 68 through 91 removed outlier: 3.557A pdb=" N VAL B 74 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B 82 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 85 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 125 removed outlier: 3.752A pdb=" N SER B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 91 removed outlier: 3.965A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 125 removed outlier: 4.937A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU C 119 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 124 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU C 125 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 3.998A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 126 removed outlier: 3.571A pdb=" N ALA D 96 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 110 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER D 117 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE D 126 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 91 removed outlier: 3.964A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 126 removed outlier: 5.321A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU E 99 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL E 100 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU E 119 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE E 122 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE E 124 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU E 125 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE E 126 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 91 removed outlier: 3.645A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 95 No H-bonds generated for 'chain 'F' and resid 93 through 95' Processing helix chain 'F' and resid 98 through 126 removed outlier: 4.146A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 89 removed outlier: 4.943A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 125 removed outlier: 3.539A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL G 100 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR G 110 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER G 112 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE G 122 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU G 125 " --> pdb=" O PHE G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 65 removed outlier: 3.898A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 91 removed outlier: 3.671A pdb=" N GLY H 73 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA H 89 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG H 91 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 126 removed outlier: 4.699A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL H 100 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR H 110 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE H 126 " --> pdb=" O LEU H 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 3.693A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 126 removed outlier: 5.173A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER I 117 " --> pdb=" O ALA I 114 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU I 119 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU I 125 " --> pdb=" O PHE I 122 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE I 126 " --> pdb=" O LEU I 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 91 removed outlier: 3.589A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 95 No H-bonds generated for 'chain 'J' and resid 93 through 95' Processing helix chain 'J' and resid 98 through 125 removed outlier: 4.119A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 119 Processing helix chain 'M' and resid 135 through 144 Processing helix chain 'M' and resid 148 through 167 removed outlier: 4.579A pdb=" N GLY M 166 " --> pdb=" O CYS M 162 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU M 167 " --> pdb=" O ASN M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 176 No H-bonds generated for 'chain 'M' and resid 174 through 176' Processing helix chain 'M' and resid 178 through 200 removed outlier: 3.725A pdb=" N LYS M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 229 removed outlier: 3.920A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 264 removed outlier: 3.699A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA M 260 " --> pdb=" O GLY M 256 " (cutoff:3.500A) removed outlier: 4.267A 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: 4.001A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 Processing helix chain 'P' and resid 69 through 83 Processing helix chain 'P' and resid 85 through 92 removed outlier: 4.054A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 Processing helix chain 'P' and resid 116 through 127 Processing helix chain 'P' and resid 130 through 148 removed outlier: 4.099A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU P 136 " --> pdb=" O ALA P 133 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 177 removed outlier: 4.126A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS P 173 " --> pdb=" O GLU P 169 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS P 176 " --> pdb=" O LYS P 172 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE P 177 " --> pdb=" O LYS P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 226 removed outlier: 3.678A pdb=" N ASN P 223 " --> pdb=" O ASN P 219 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS P 224 " --> pdb=" O ASN P 220 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU P 225 " --> pdb=" O PHE P 221 " (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: 3.624A pdb=" N ASN Q 29 " --> pdb=" O ASP Q 25 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 43 removed outlier: 3.815A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN Q 43 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 38 removed outlier: 3.818A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 169 removed outlier: 3.762A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 194 removed outlier: 3.771A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 78 removed outlier: 3.632A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 88 Processing helix chain 'S' and resid 116 through 130 removed outlier: 3.511A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 150 Processing helix chain 'S' and resid 172 through 183 Processing helix chain 'S' and resid 213 through 220 removed outlier: 5.713A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 239 through 312 removed outlier: 3.520A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS S 279 " --> pdb=" O GLU S 275 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 75 removed outlier: 3.547A pdb=" N LYS T 65 " --> pdb=" O HIS T 61 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE T 67 " --> pdb=" O SER T 63 " (cutoff:3.500A) Proline residue: T 68 - end of helix removed outlier: 4.130A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) removed outlier: 3.685A 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 207 through 212 Processing helix chain 'T' and resid 231 through 246 Processing helix chain 'T' and resid 266 through 278 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 315 Proline residue: T 303 - end of helix removed outlier: 4.264A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 354 through 364 removed outlier: 3.538A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU T 363 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG T 364 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 Processing helix chain 'T' and resid 410 through 413 No H-bonds generated for 'chain 'T' and resid 410 through 413' Processing helix chain 'T' and resid 431 through 434 Processing helix chain 'T' and resid 437 through 442 Processing helix chain 'T' and resid 444 through 457 Processing helix chain 'T' and resid 470 through 483 Processing helix chain 'T' and resid 494 through 505 removed outlier: 3.664A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 527 removed outlier: 4.170A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 Processing helix chain 'T' and resid 544 through 555 removed outlier: 3.787A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 48 No H-bonds generated for 'chain 'U' and resid 46 through 48' Processing helix chain 'U' and resid 62 through 71 removed outlier: 4.926A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix Processing helix chain 'U' and resid 157 through 159 No H-bonds generated for 'chain 'U' and resid 157 through 159' Processing helix chain 'U' and resid 207 through 212 Processing helix chain 'U' and resid 231 through 247 removed outlier: 3.660A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 279 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 316 Proline residue: U 303 - end of helix removed outlier: 4.096A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR U 316 " --> pdb=" O TYR U 312 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 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 354 through 364 removed outlier: 4.556A pdb=" N ARG U 364 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 393 through 401 Processing helix chain 'U' and resid 411 through 414 No H-bonds generated for 'chain 'U' and resid 411 through 414' Processing helix chain 'U' and resid 437 through 459 removed outlier: 4.543A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR U 453 " --> pdb=" O GLU U 449 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE U 459 " --> pdb=" O GLU U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 468 through 484 removed outlier: 3.694A pdb=" N TYR U 472 " --> pdb=" O ALA U 468 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL U 473 " --> pdb=" O ALA U 469 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET U 483 " --> pdb=" O ARG U 479 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 505 removed outlier: 3.897A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 527 removed outlier: 3.707A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 539 removed outlier: 3.966A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 544 through 555 removed outlier: 3.710A pdb=" N ARG U 555 " --> pdb=" O LYS U 551 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 48 No H-bonds generated for 'chain 'V' and resid 46 through 48' Processing helix chain 'V' and resid 58 through 66 removed outlier: 3.877A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 210 No H-bonds generated for 'chain 'V' and resid 207 through 210' Processing helix chain 'V' and resid 231 through 246 removed outlier: 3.895A pdb=" N GLN V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 284 Processing helix chain 'V' and resid 296 through 314 Proline residue: V 303 - end of helix removed outlier: 3.907A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 341 removed outlier: 3.569A pdb=" N LEU V 341 " --> pdb=" O MET V 337 " (cutoff:3.500A) 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: 3.981A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) removed outlier: 3.722A 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 401 Processing helix chain 'V' and resid 431 through 433 No H-bonds generated for 'chain 'V' and resid 431 through 433' Processing helix chain 'V' and resid 439 through 455 removed outlier: 4.146A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 483 removed outlier: 3.507A pdb=" N ALA V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 505 removed outlier: 3.530A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) Processing helix chain 'V' and resid 517 through 527 removed outlier: 4.266A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 539 removed outlier: 3.812A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 549 through 553 Processing helix chain 'X' and resid 150 through 152 No H-bonds generated for 'chain 'X' and resid 150 through 152' Processing helix chain 'X' and resid 166 through 169 No H-bonds generated for 'chain 'X' and resid 166 through 169' Processing helix chain 'X' and resid 189 through 203 Processing helix chain 'X' and resid 217 through 230 Processing helix chain 'X' and resid 236 through 241 removed outlier: 4.566A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 258 No H-bonds generated for 'chain 'X' and resid 255 through 258' Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.914A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 300 Processing helix chain 'X' and resid 315 through 322 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 Processing helix chain 'X' and resid 366 through 370 Processing helix chain 'X' and resid 389 through 392 No H-bonds generated for 'chain 'X' and resid 389 through 392' Processing helix chain 'X' and resid 394 through 412 removed outlier: 3.883A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) Processing helix chain 'X' and resid 414 through 420 removed outlier: 3.940A pdb=" N ALA X 418 " --> pdb=" O GLN X 414 " (cutoff:3.500A) Processing helix chain 'X' and resid 427 through 442 removed outlier: 3.556A pdb=" N LEU X 431 " --> pdb=" O GLU X 427 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 463 through 475 removed outlier: 3.741A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) Processing helix chain 'X' and resid 492 through 508 removed outlier: 4.268A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP X 505 " --> pdb=" O LYS X 501 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE X 506 " --> pdb=" O MET X 502 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA X 507 " --> pdb=" O ALA X 503 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 533 removed outlier: 3.615A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 189 through 200 Processing helix chain 'Y' and resid 217 through 230 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 3.833A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 258 No H-bonds generated for 'chain 'Y' and resid 255 through 258' Processing helix chain 'Y' and resid 261 through 274 removed outlier: 3.610A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 297 Processing helix chain 'Y' and resid 314 through 322 Processing helix chain 'Y' and resid 349 through 357 removed outlier: 3.759A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 371 removed outlier: 3.932A pdb=" N LEU Y 371 " --> pdb=" O SER Y 367 " (cutoff:3.500A) Processing helix chain 'Y' and resid 394 through 419 removed outlier: 3.804A pdb=" N LEU Y 413 " --> pdb=" O ASP Y 409 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN Y 414 " --> pdb=" O TYR Y 410 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 422 through 424 No H-bonds generated for 'chain 'Y' and resid 422 through 424' Processing helix chain 'Y' and resid 427 through 443 removed outlier: 3.873A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) Processing helix chain 'Y' and resid 450 through 454 removed outlier: 3.870A pdb=" N THR Y 454 " --> pdb=" O GLU Y 451 " (cutoff:3.500A) Processing helix chain 'Y' and resid 463 through 475 Processing helix chain 'Y' and resid 483 through 485 No H-bonds generated for 'chain 'Y' and resid 483 through 485' Processing helix chain 'Y' and resid 492 through 504 removed outlier: 4.020A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) Processing helix chain 'Y' and resid 512 through 514 No H-bonds generated for 'chain 'Y' and resid 512 through 514' Processing helix chain 'Y' and resid 527 through 532 Processing helix chain 'Y' and resid 542 through 544 No H-bonds generated for 'chain 'Y' and resid 542 through 544' Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 165 through 170 Processing helix chain 'Z' and resid 189 through 197 Processing helix chain 'Z' and resid 217 through 229 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 3.929A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 5.008A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 297 removed outlier: 3.611A pdb=" N GLU Z 296 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) Processing helix chain 'Z' and resid 315 through 324 removed outlier: 4.847A pdb=" N ARG Z 324 " --> pdb=" O GLY Z 320 " (cutoff:3.500A) Processing helix chain 'Z' and resid 342 through 344 No H-bonds generated for 'chain 'Z' and resid 342 through 344' Processing helix chain 'Z' and resid 349 through 355 removed outlier: 3.795A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE Z 355 " --> pdb=" O PRO Z 351 " (cutoff:3.500A) Processing helix chain 'Z' and resid 366 through 370 Processing helix chain 'Z' and resid 385 through 387 No H-bonds generated for 'chain 'Z' and resid 385 through 387' Processing helix chain 'Z' and resid 389 through 392 No H-bonds generated for 'chain 'Z' and resid 389 through 392' Processing helix chain 'Z' and resid 394 through 417 removed outlier: 4.353A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 430 through 442 Processing helix chain 'Z' and resid 449 through 451 No H-bonds generated for 'chain 'Z' and resid 449 through 451' Processing helix chain 'Z' and resid 463 through 475 Processing helix chain 'Z' and resid 484 through 486 No H-bonds generated for 'chain 'Z' and resid 484 through 486' Processing helix chain 'Z' and resid 492 through 506 removed outlier: 3.942A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 removed outlier: 4.220A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '1' and resid 183 through 185 removed outlier: 4.356A pdb=" N VAL 1 226 " --> pdb=" O ALA 1 185 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 369 through 372 removed outlier: 3.509A pdb=" N ALA 2 375 " --> pdb=" O LYS 2 372 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL 2 382 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '7' and resid 35 through 41 removed outlier: 3.797A pdb=" N GLU 7 47 " --> pdb=" O ALA 7 40 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA 7 52 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 187 through 190 removed outlier: 3.705A 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: 6.781A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.377A 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: 4.394A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'S' and resid 203 through 211 removed outlier: 3.584A pdb=" N VAL S 101 " --> pdb=" O SER S 189 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.524A 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: 4.121A pdb=" N LYS T 116 " --> pdb=" O PHE T 132 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLY T 128 " --> pdb=" O LEU T 120 " (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 382 through 384 removed outlier: 6.731A pdb=" N ILE T 223 " --> pdb=" O ILE T 383 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE T 406 " --> pdb=" O ILE T 224 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'T' and resid 285 through 290 removed outlier: 9.029A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE T 380 " --> pdb=" O TYR T 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.724A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= O, first strand: chain 'U' and resid 223 through 225 Processing sheet with id= P, first strand: chain 'U' and resid 286 through 290 removed outlier: 7.102A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V' and resid 85 through 91 removed outlier: 6.620A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL V 90 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE V 94 " --> pdb=" O VAL V 90 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLN V 149 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N CYS V 110 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR V 147 " --> pdb=" O CYS V 110 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= S, first strand: chain 'V' and resid 404 through 408 removed outlier: 3.739A pdb=" N LEU V 222 " --> pdb=" O GLY V 404 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE V 383 " --> pdb=" O ILE V 223 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.855A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'X' and resid 38 through 44 removed outlier: 6.387A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'X' and resid 110 through 113 Processing sheet with id= W, first strand: chain 'X' and resid 360 through 363 removed outlier: 8.309A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL X 284 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL X 213 " --> pdb=" O ASP X 285 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N THR X 245 " --> pdb=" O PHE X 210 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLY X 212 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL X 247 " --> pdb=" O GLY X 212 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY X 214 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY X 249 " --> pdb=" O GLY X 214 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= Y, first strand: chain 'Y' and resid 37 through 39 removed outlier: 6.648A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ARG Y 51 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id= AA, first strand: chain 'Y' and resid 360 through 363 removed outlier: 7.548A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL Y 280 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU Y 282 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA Y 338 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL Y 284 " --> pdb=" O ALA Y 338 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 39 through 44 removed outlier: 6.529A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.517A pdb=" N ASP Z 139 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Z' and resid 360 through 363 removed outlier: 6.394A pdb=" N THR Z 245 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY Z 212 " --> pdb=" O THR Z 245 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL Z 247 " --> pdb=" O GLY Z 212 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 559 through 561 2452 hydrogen bonds defined for protein. 6609 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.35 Time building geometry restraints manager: 17.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16513 1.34 - 1.46: 8101 1.46 - 1.57: 29769 1.57 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54658 Sorted by residual: bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.66e+01 bond pdb=" C5 ATP T1001 " pdb=" C6 ATP T1001 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.43e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.33e+01 ... (remaining 54653 not shown) Histogram of bond angle deviations from ideal: 96.86 - 104.69: 905 104.69 - 112.52: 28327 112.52 - 120.35: 24445 120.35 - 128.17: 20154 128.17 - 136.00: 290 Bond angle restraints: 74121 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 118.86 21.01 1.00e+00 1.00e+00 4.41e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 119.84 20.03 1.00e+00 1.00e+00 4.01e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 117.80 19.03 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 119.16 17.67 1.00e+00 1.00e+00 3.12e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 124.43 15.44 1.00e+00 1.00e+00 2.38e+02 ... (remaining 74116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 30882 22.60 - 45.21: 1860 45.21 - 67.81: 196 67.81 - 90.42: 65 90.42 - 113.02: 2 Dihedral angle restraints: 33005 sinusoidal: 12661 harmonic: 20344 Sorted by residual: dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -127.06 -52.94 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -131.19 -48.81 0 5.00e+00 4.00e-02 9.53e+01 dihedral pdb=" CA LYS 5 119 " pdb=" C LYS 5 119 " pdb=" N PRO 5 120 " pdb=" CA PRO 5 120 " ideal model delta harmonic sigma weight residual -180.00 -148.29 -31.71 0 5.00e+00 4.00e-02 4.02e+01 ... (remaining 33002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 7580 0.078 - 0.157: 1041 0.157 - 0.235: 50 0.235 - 0.313: 10 0.313 - 0.392: 2 Chirality restraints: 8683 Sorted by residual: chirality pdb=" CB VAL 2 357 " pdb=" CA VAL 2 357 " pdb=" CG1 VAL 2 357 " pdb=" CG2 VAL 2 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CB VAL 2 41 " pdb=" CA VAL 2 41 " pdb=" CG1 VAL 2 41 " pdb=" CG2 VAL 2 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CB ILE Z 524 " pdb=" CA ILE Z 524 " pdb=" CG1 ILE Z 524 " pdb=" CG2 ILE Z 524 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 8680 not shown) Planarity restraints: 9504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 503 " 0.031 2.00e-02 2.50e+03 6.11e-02 3.73e+01 pdb=" C ALA Y 503 " -0.106 2.00e-02 2.50e+03 pdb=" O ALA Y 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Y 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.04e-02 3.65e+01 pdb=" C ALA Z 503 " -0.105 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 33 " -0.051 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO Q 34 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO Q 34 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO Q 34 " -0.043 5.00e-02 4.00e+02 ... (remaining 9501 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 494 2.57 - 3.15: 41599 3.15 - 3.73: 86004 3.73 - 4.32: 119077 4.32 - 4.90: 196507 Nonbonded interactions: 443681 Sorted by model distance: nonbonded pdb=" O ASN Z 514 " pdb=" CG2 VAL Z 517 " model vdw 1.985 3.460 nonbonded pdb=" O2B ATP V1001 " pdb="MG MG V1002 " model vdw 2.054 2.170 nonbonded pdb=" O1B ATP U1001 " pdb="MG MG U1002 " model vdw 2.058 2.170 nonbonded pdb=" OG1 THR Y 190 " pdb="MG MG Y 602 " model vdw 2.068 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.090 2.170 ... (remaining 443676 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 562 or resid 1001 through 1002)) selection = chain 'V' } ncs_group { reference = (chain 'X' and resid 37 through 552) selection = (chain 'Y' and resid 37 through 552) selection = (chain 'Z' and resid 37 through 552) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 23.450 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 112.540 Find NCS groups from input model: 2.490 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 54658 Z= 0.366 Angle : 0.864 21.011 74121 Z= 0.504 Chirality : 0.053 0.392 8683 Planarity : 0.007 0.077 9504 Dihedral : 14.608 113.020 19929 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.32 % Favored : 95.51 % Rotamer: Outliers : 0.21 % Allowed : 8.49 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.08), residues: 7034 helix: -2.83 (0.06), residues: 3769 sheet: -2.38 (0.20), residues: 550 loop : -2.38 (0.10), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 4 206 HIS 0.011 0.001 HIS R 66 PHE 0.026 0.002 PHE 3 115 TYR 0.026 0.002 TYR 7 119 ARG 0.006 0.001 ARG T 555 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1556 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1544 time to evaluate : 4.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 1553 average time/residue: 0.5896 time to fit residues: 1509.1850 Evaluate side-chains 828 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 823 time to evaluate : 4.620 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4087 time to fit residues: 10.0695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 588 optimal weight: 10.0000 chunk 528 optimal weight: 9.9990 chunk 293 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 356 optimal weight: 2.9990 chunk 282 optimal weight: 7.9990 chunk 546 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 332 optimal weight: 6.9990 chunk 406 optimal weight: 4.9990 chunk 632 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN 0 44 ASN 1 285 GLN 1 316 ASN 1 365 GLN ** 1 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 68 ASN 2 74 ASN 2 153 ASN 2 243 GLN 2 289 HIS 3 87 ASN 3 176 GLN 3 309 ASN 4 38 GLN 4 240 GLN ** 4 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 109 GLN 6 40 ASN ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 97 HIS 6 109 GLN 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 26 HIS 9 97 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 98 GLN M 108 ASN M 121 ASN ** M 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 HIS P 220 ASN R 73 ASN R 83 GLN R 181 ASN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 174 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 257 ASN S 262 ASN S 297 GLN T 64 GLN ** T 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 104 GLN U 123 GLN ** U 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 248 GLN U 264 GLN U 319 HIS ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 GLN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS V 149 GLN ** V 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 GLN V 228 GLN V 242 GLN V 244 ASN V 264 GLN V 271 GLN V 278 GLN V 386 GLN V 486 GLN V 515 GLN X 42 GLN X 78 GLN ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 157 GLN X 199 ASN X 278 GLN X 294 ASN X 322 GLN X 404 GLN X 448 GLN ** X 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 174 GLN Y 199 ASN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 42 GLN Z 68 HIS Z 174 GLN Z 204 HIS Z 278 GLN ** Z 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 408 GLN ** Z 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 562 ASN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 54658 Z= 0.354 Angle : 0.702 13.587 74121 Z= 0.361 Chirality : 0.046 0.429 8683 Planarity : 0.005 0.066 9504 Dihedral : 6.394 96.789 7664 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.59 % Favored : 95.28 % Rotamer: Outliers : 3.77 % Allowed : 17.64 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.09), residues: 7034 helix: -1.21 (0.08), residues: 3802 sheet: -1.94 (0.19), residues: 595 loop : -1.78 (0.11), residues: 2637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 4 206 HIS 0.009 0.001 HIS V 241 PHE 0.026 0.002 PHE I 107 TYR 0.028 0.002 TYR Q 16 ARG 0.011 0.001 ARG 7 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 885 time to evaluate : 4.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 212 outliers final: 129 residues processed: 1027 average time/residue: 0.5323 time to fit residues: 938.5589 Evaluate side-chains 838 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 709 time to evaluate : 4.668 Switching outliers to nearest non-outliers outliers start: 129 outliers final: 0 residues processed: 129 average time/residue: 0.3959 time to fit residues: 103.4066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 351 optimal weight: 9.9990 chunk 196 optimal weight: 0.9990 chunk 526 optimal weight: 10.0000 chunk 431 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 634 optimal weight: 2.9990 chunk 685 optimal weight: 8.9990 chunk 564 optimal weight: 1.9990 chunk 628 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 chunk 508 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 590 HIS 2 153 ASN 4 68 HIS ** 4 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 109 GLN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN G 98 GLN H 87 ASN ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN R 110 GLN R 181 ASN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 GLN T 271 GLN T 441 GLN ** U 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 405 GLN ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 408 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 54658 Z= 0.241 Angle : 0.611 12.204 74121 Z= 0.311 Chirality : 0.043 0.287 8683 Planarity : 0.004 0.054 9504 Dihedral : 6.009 90.158 7664 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.78 % Rotamer: Outliers : 2.13 % Allowed : 19.99 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.10), residues: 7034 helix: -0.58 (0.08), residues: 3823 sheet: -1.59 (0.20), residues: 583 loop : -1.48 (0.12), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 5 21 HIS 0.011 0.001 HIS Z 396 PHE 0.028 0.002 PHE J 107 TYR 0.027 0.002 TYR 4 211 ARG 0.009 0.000 ARG X 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 838 time to evaluate : 4.837 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: 120 outliers final: 50 residues processed: 924 average time/residue: 0.4997 time to fit residues: 793.9649 Evaluate side-chains 759 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 709 time to evaluate : 4.649 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.4097 time to fit residues: 43.9565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 626 optimal weight: 0.0570 chunk 476 optimal weight: 9.9990 chunk 329 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 302 optimal weight: 2.9990 chunk 425 optimal weight: 10.0000 chunk 636 optimal weight: 4.9990 chunk 673 optimal weight: 6.9990 chunk 332 optimal weight: 6.9990 chunk 603 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 overall best weight: 1.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 531 HIS ** 4 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 97 HIS 6 109 GLN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN M 243 ASN P 45 GLN R 110 GLN ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 ASN ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 435 GLN ** U 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 174 GLN ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 337 GLN ** X 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 54658 Z= 0.210 Angle : 0.586 11.489 74121 Z= 0.297 Chirality : 0.043 0.285 8683 Planarity : 0.004 0.050 9504 Dihedral : 5.745 83.935 7664 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 2.33 % Allowed : 21.59 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.10), residues: 7034 helix: -0.22 (0.08), residues: 3813 sheet: -1.36 (0.21), residues: 577 loop : -1.24 (0.12), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 8 45 HIS 0.010 0.001 HIS Z 396 PHE 0.034 0.001 PHE Y 470 TYR 0.032 0.001 TYR S 166 ARG 0.007 0.000 ARG U 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 790 time to evaluate : 4.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 67 residues processed: 878 average time/residue: 0.5038 time to fit residues: 766.7619 Evaluate side-chains 770 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 703 time to evaluate : 4.634 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.3950 time to fit residues: 56.7721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 561 optimal weight: 0.9980 chunk 382 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 501 optimal weight: 0.7980 chunk 277 optimal weight: 3.9990 chunk 574 optimal weight: 9.9990 chunk 465 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 344 optimal weight: 7.9990 chunk 604 optimal weight: 4.9990 chunk 170 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 409 GLN ** 4 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 170 HIS ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN R 110 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 ASN ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 153 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 42 GLN ** Z 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 54658 Z= 0.172 Angle : 0.566 10.415 74121 Z= 0.285 Chirality : 0.042 0.272 8683 Planarity : 0.004 0.050 9504 Dihedral : 5.503 82.791 7664 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.93 % Rotamer: Outliers : 1.72 % Allowed : 22.14 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.10), residues: 7034 helix: 0.07 (0.09), residues: 3801 sheet: -1.03 (0.21), residues: 573 loop : -1.12 (0.12), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 8 45 HIS 0.012 0.001 HIS Z 396 PHE 0.027 0.001 PHE I 107 TYR 0.028 0.001 TYR 4 211 ARG 0.006 0.000 ARG U 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 801 time to evaluate : 4.778 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: 97 outliers final: 34 residues processed: 870 average time/residue: 0.5022 time to fit residues: 763.6868 Evaluate side-chains 728 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 694 time to evaluate : 4.678 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4125 time to fit residues: 32.5987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 226 optimal weight: 0.0770 chunk 606 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 395 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 674 optimal weight: 1.9990 chunk 559 optimal weight: 8.9990 chunk 312 optimal weight: 0.0370 chunk 56 optimal weight: 4.9990 chunk 223 optimal weight: 0.7980 chunk 354 optimal weight: 4.9990 overall best weight: 1.1820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 97 HIS ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 GLN R 137 HIS ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 123 GLN U 358 HIS ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 278 GLN ** X 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 153 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 54658 Z= 0.170 Angle : 0.564 10.137 74121 Z= 0.284 Chirality : 0.042 0.304 8683 Planarity : 0.004 0.049 9504 Dihedral : 5.348 80.429 7664 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 1.46 % Allowed : 23.65 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.10), residues: 7034 helix: 0.25 (0.09), residues: 3806 sheet: -0.86 (0.22), residues: 592 loop : -1.03 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP 9 77 HIS 0.015 0.001 HIS V 241 PHE 0.033 0.001 PHE 0 12 TYR 0.027 0.001 TYR 4 211 ARG 0.007 0.000 ARG U 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 771 time to evaluate : 4.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 39 residues processed: 816 average time/residue: 0.4990 time to fit residues: 707.2578 Evaluate side-chains 739 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 700 time to evaluate : 4.648 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3819 time to fit residues: 34.7393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 650 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 384 optimal weight: 3.9990 chunk 492 optimal weight: 5.9990 chunk 381 optimal weight: 8.9990 chunk 567 optimal weight: 6.9990 chunk 376 optimal weight: 3.9990 chunk 671 optimal weight: 0.0980 chunk 420 optimal weight: 5.9990 chunk 409 optimal weight: 0.9980 chunk 310 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 408 GLN ** 4 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 56 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN R 110 GLN R 137 HIS ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 435 GLN ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 GLN ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 278 GLN ** X 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 HIS Y 153 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 54658 Z= 0.199 Angle : 0.576 12.019 74121 Z= 0.288 Chirality : 0.043 0.289 8683 Planarity : 0.004 0.049 9504 Dihedral : 5.318 77.610 7664 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.31 % Favored : 95.59 % Rotamer: Outliers : 1.14 % Allowed : 24.47 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.10), residues: 7034 helix: 0.35 (0.09), residues: 3800 sheet: -0.79 (0.22), residues: 586 loop : -0.97 (0.12), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP 9 77 HIS 0.013 0.001 HIS Z 396 PHE 0.030 0.001 PHE I 107 TYR 0.026 0.001 TYR 4 211 ARG 0.008 0.000 ARG X 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 730 time to evaluate : 4.709 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: 64 outliers final: 30 residues processed: 777 average time/residue: 0.5225 time to fit residues: 707.5677 Evaluate side-chains 708 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 678 time to evaluate : 4.622 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4112 time to fit residues: 29.7883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 415 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 401 optimal weight: 6.9990 chunk 202 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 427 optimal weight: 5.9990 chunk 457 optimal weight: 4.9990 chunk 332 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 528 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 245 GLN 6 97 HIS ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 56 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 ASN Q 40 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 GLN R 137 HIS ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 HIS U 60 GLN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN U 527 GLN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 408 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 54658 Z= 0.283 Angle : 0.638 12.793 74121 Z= 0.321 Chirality : 0.044 0.311 8683 Planarity : 0.004 0.049 9504 Dihedral : 5.520 83.981 7664 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.22 % Favored : 94.67 % Rotamer: Outliers : 1.56 % Allowed : 24.38 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.10), residues: 7034 helix: 0.26 (0.09), residues: 3804 sheet: -0.88 (0.22), residues: 595 loop : -1.01 (0.12), residues: 2635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP 9 77 HIS 0.014 0.001 HIS Z 396 PHE 0.029 0.002 PHE Y 470 TYR 0.025 0.002 TYR 4 211 ARG 0.007 0.000 ARG U 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 703 time to evaluate : 4.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 50 residues processed: 752 average time/residue: 0.5280 time to fit residues: 690.3111 Evaluate side-chains 712 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 662 time to evaluate : 4.711 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.4288 time to fit residues: 46.3307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 611 optimal weight: 7.9990 chunk 643 optimal weight: 0.0470 chunk 587 optimal weight: 4.9990 chunk 626 optimal weight: 0.8980 chunk 376 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 491 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 565 optimal weight: 0.9980 chunk 592 optimal weight: 0.7980 chunk 623 optimal weight: 2.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 153 ASN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 56 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 GLN R 137 HIS ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 527 GLN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 GLN X 250 GLN ** X 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 408 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 54658 Z= 0.175 Angle : 0.590 13.198 74121 Z= 0.295 Chirality : 0.043 0.353 8683 Planarity : 0.004 0.049 9504 Dihedral : 5.292 82.872 7664 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.01 % Favored : 95.89 % Rotamer: Outliers : 0.76 % Allowed : 25.02 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.10), residues: 7034 helix: 0.45 (0.09), residues: 3803 sheet: -0.76 (0.22), residues: 586 loop : -0.89 (0.12), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP 9 77 HIS 0.015 0.001 HIS Z 396 PHE 0.023 0.001 PHE U 276 TYR 0.027 0.001 TYR 4 211 ARG 0.008 0.000 ARG U 227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 736 time to evaluate : 4.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 16 residues processed: 761 average time/residue: 0.5167 time to fit residues: 682.3085 Evaluate side-chains 691 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 675 time to evaluate : 4.687 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4039 time to fit residues: 18.5599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 411 optimal weight: 1.9990 chunk 661 optimal weight: 10.0000 chunk 404 optimal weight: 10.0000 chunk 314 optimal weight: 10.0000 chunk 460 optimal weight: 20.0000 chunk 694 optimal weight: 3.9990 chunk 639 optimal weight: 0.4980 chunk 552 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 427 optimal weight: 0.0770 chunk 339 optimal weight: 20.0000 overall best weight: 2.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 97 HIS ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 56 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN R 110 GLN R 137 HIS ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 358 HIS ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 397 ASN ** X 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 408 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 54658 Z= 0.242 Angle : 0.628 12.482 74121 Z= 0.314 Chirality : 0.044 0.346 8683 Planarity : 0.004 0.048 9504 Dihedral : 5.335 80.358 7664 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.06 % Favored : 94.83 % Rotamer: Outliers : 0.50 % Allowed : 25.66 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.10), residues: 7034 helix: 0.40 (0.09), residues: 3812 sheet: -0.79 (0.22), residues: 574 loop : -0.87 (0.12), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP 9 77 HIS 0.015 0.001 HIS Z 396 PHE 0.036 0.002 PHE 0 12 TYR 0.029 0.001 TYR M 229 ARG 0.010 0.000 ARG X 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 692 time to evaluate : 4.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 703 average time/residue: 0.5339 time to fit residues: 653.7665 Evaluate side-chains 682 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 666 time to evaluate : 4.696 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4631 time to fit residues: 19.5953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 439 optimal weight: 0.5980 chunk 589 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 509 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 553 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 568 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 231 HIS ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 312 HIS ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN R 110 GLN ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN U 358 HIS ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 397 ASN ** X 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 408 GLN ** X 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 42 GLN ** Z 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.119894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100767 restraints weight = 121285.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.100891 restraints weight = 107333.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.101433 restraints weight = 89587.280| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 54658 Z= 0.328 Angle : 0.686 12.751 74121 Z= 0.344 Chirality : 0.046 0.336 8683 Planarity : 0.004 0.054 9504 Dihedral : 5.617 81.020 7664 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.50 % Favored : 94.38 % Rotamer: Outliers : 0.69 % Allowed : 25.69 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.10), residues: 7034 helix: 0.22 (0.08), residues: 3810 sheet: -0.95 (0.22), residues: 568 loop : -0.95 (0.12), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP 9 77 HIS 0.015 0.002 HIS Z 396 PHE 0.036 0.002 PHE 0 12 TYR 0.031 0.002 TYR M 229 ARG 0.010 0.001 ARG X 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12642.16 seconds wall clock time: 223 minutes 28.52 seconds (13408.52 seconds total)