Starting phenix.real_space_refine on Tue Feb 13 06:05:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdl_4822/02_2024/6rdl_4822_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdl_4822/02_2024/6rdl_4822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdl_4822/02_2024/6rdl_4822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdl_4822/02_2024/6rdl_4822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdl_4822/02_2024/6rdl_4822_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdl_4822/02_2024/6rdl_4822_updated.pdb" } resolution = 3.7 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34297 2.51 5 N 9112 2.21 5 O 10171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 46": "OE1" <-> "OE2" Residue "1 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 69": "OD1" <-> "OD2" Residue "1 ASP 72": "OD1" <-> "OD2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 GLU 165": "OE1" <-> "OE2" Residue "1 ASP 172": "OD1" <-> "OD2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 GLU 198": "OE1" <-> "OE2" Residue "1 GLU 215": "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 334": "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 GLU 414": "OE1" <-> "OE2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 GLU 457": "OE1" <-> "OE2" Residue "1 GLU 507": "OE1" <-> "OE2" Residue "1 GLU 513": "OE1" <-> "OE2" Residue "1 ASP 539": "OD1" <-> "OD2" Residue "1 ASP 549": "OD1" <-> "OD2" Residue "1 ASP 572": "OD1" <-> "OD2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 79": "OE1" <-> "OE2" Residue "2 GLU 86": "OE1" <-> "OE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 171": "OD1" <-> "OD2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 ASP 189": "OD1" <-> "OD2" Residue "2 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 278": "OD1" <-> "OD2" Residue "2 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 316": "OD1" <-> "OD2" Residue "2 PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 346": "NH1" <-> "NH2" Residue "2 GLU 348": "OE1" <-> "OE2" Residue "2 ASP 374": "OD1" <-> "OD2" 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 GLU 93": "OE1" <-> "OE2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 ASP 154": "OD1" <-> "OD2" Residue "3 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 213": "NH1" <-> "NH2" Residue "3 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 233": "NH1" <-> "NH2" Residue "3 ARG 242": "NH1" <-> "NH2" Residue "3 ARG 257": "NH1" <-> "NH2" Residue "3 ASP 259": "OD1" <-> "OD2" Residue "3 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 54": "OE1" <-> "OE2" 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 GLU 104": "OE1" <-> "OE2" Residue "4 ASP 121": "OD1" <-> "OD2" Residue "4 TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 133": "OD1" <-> "OD2" Residue "4 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 176": "NH1" <-> "NH2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 202": "OE1" <-> "OE2" Residue "4 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 225": "OE1" <-> "OE2" Residue "4 ASP 231": "OD1" <-> "OD2" Residue "4 ARG 232": "NH1" <-> "NH2" Residue "4 ARG 255": "NH1" <-> "NH2" Residue "4 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 ASP 63": "OD1" <-> "OD2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 91": "OD1" <-> "OD2" Residue "6 PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 164": "NH1" <-> "NH2" Residue "7 ARG 165": "NH1" <-> "NH2" Residue "7 ARG 166": "NH1" <-> "NH2" Residue "7 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 13": "NH1" <-> "NH2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "8 ASP 66": "OD1" <-> "OD2" Residue "8 TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 6": "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 ASP 17": "OD1" <-> "OD2" Residue "9 GLU 22": "OE1" <-> "OE2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 40": "NH1" <-> "NH2" Residue "9 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 74": "OE1" <-> "OE2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M ASP 132": "OD1" <-> "OD2" Residue "M ARG 145": "NH1" <-> "NH2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 239": "NH1" <-> "NH2" Residue "M PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 73": "OE1" <-> "OE2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 25": "OD1" <-> "OD2" 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 "R GLU 23": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" 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 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 232": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ASP 41": "OD1" <-> "OD2" Residue "T GLU 47": "OE1" <-> "OE2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 72": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 142": "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 TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 294": "OD1" <-> "OD2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T ASP 326": "OD1" <-> "OD2" Residue "T ASP 403": "OD1" <-> "OD2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 112": "OD1" <-> "OD2" Residue "U ASP 135": "OD1" <-> "OD2" Residue "U TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ASP 165": "OD1" <-> "OD2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U GLU 221": "OE1" <-> "OE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U 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 409": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U GLU 482": "OE1" <-> "OE2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V ASP 210": "OD1" <-> "OD2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V ASP 237": "OD1" <-> "OD2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 259": "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 TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 347": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V GLU 455": "OE1" <-> "OE2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 465": "OD1" <-> "OD2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V GLU 522": "OE1" <-> "OE2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ASP 36": "OD1" <-> "OD2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X GLU 146": "OE1" <-> "OE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 168": "OD1" <-> "OD2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 218": "NH1" <-> "NH2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X ARG 225": "NH1" <-> "NH2" Residue "X ARG 239": "NH1" <-> "NH2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ASP 381": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X GLU 424": "OE1" <-> "OE2" Residue "X ASP 480": "OD1" <-> "OD2" Residue "X PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 491": "OD1" <-> "OD2" Residue "X GLU 494": "OE1" <-> "OE2" Residue "X GLU 497": "OE1" <-> "OE2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 533": "OE1" <-> "OE2" Residue "X GLU 536": "OE1" <-> "OE2" Residue "X GLU 546": "OE1" <-> "OE2" Residue "X GLU 552": "OE1" <-> "OE2" Residue "Y TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ASP 82": "OD1" <-> "OD2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ASP 91": "OD1" <-> "OD2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ARG 145": "NH1" <-> "NH2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 366": "NH1" <-> "NH2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ASP 409": "OD1" <-> "OD2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 511": "OE1" <-> "OE2" Residue "Y GLU 519": "OE1" <-> "OE2" Residue "Y ASP 523": "OD1" <-> "OD2" Residue "Y GLU 533": "OE1" <-> "OE2" Residue "Y GLU 546": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 98": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z ASP 130": "OD1" <-> "OD2" Residue "Z GLU 156": "OE1" <-> "OE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 216": "NH1" <-> "NH2" Residue "Z ASP 222": "OD1" <-> "OD2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z ARG 289": "NH1" <-> "NH2" Residue "Z GLU 323": "OE1" <-> "OE2" Residue "Z ASP 348": "OD1" <-> "OD2" Residue "Z PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 415": "OD1" <-> "OD2" Residue "Z GLU 427": "OE1" <-> "OE2" Residue "Z ARG 435": "NH1" <-> "NH2" Residue "Z ARG 437": "NH1" <-> "NH2" Residue "Z PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 465": "OD1" <-> "OD2" Residue "Z ASP 480": "OD1" <-> "OD2" Residue "Z GLU 497": "OE1" <-> "OE2" Residue "Z ASP 500": "OD1" <-> "OD2" Residue "Z ASP 505": "OD1" <-> "OD2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z ASP 523": "OD1" <-> "OD2" Residue "Z GLU 536": "OE1" <-> "OE2" Residue "Z GLU 541": "OE1" <-> "OE2" Residue "Z ASP 543": "OD1" <-> "OD2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 552": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 53748 Number of models: 1 Model: "" Number of chains: 37 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.97, per 1000 atoms: 0.39 Number of scatterers: 53748 At special positions: 0 Unit cell: (212.706, 134.784, 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 10171 8.00 N 9112 7.00 C 34297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.53 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 290 helices and 31 sheets defined 51.2% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.53 Creating SS restraints... Processing helix chain '0' and resid 4 through 7 No H-bonds generated for 'chain '0' and resid 4 through 7' Processing helix chain '0' and resid 18 through 30 Processing helix chain '0' and resid 44 through 49 Processing helix chain '0' and resid 52 through 55 No H-bonds generated for 'chain '0' and resid 52 through 55' Processing helix chain '1' and resid 46 through 71 Processing helix chain '1' and resid 107 through 141 Processing helix chain '1' and resid 164 through 178 removed outlier: 4.150A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA 1 177 " --> pdb=" O LYS 1 173 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU 1 178 " --> pdb=" O TYR 1 174 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 204 removed outlier: 3.924A pdb=" N VAL 1 204 " --> pdb=" O PHE 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 207 through 223 removed outlier: 5.245A pdb=" N SER 1 211 " --> pdb=" O LYS 1 208 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL 1 213 " --> pdb=" O ALA 1 210 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU 1 223 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 242 through 270 Processing helix chain '1' and resid 272 through 276 removed outlier: 3.801A 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 295 through 306 removed outlier: 3.519A pdb=" N GLN 1 298 " --> pdb=" O PRO 1 295 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLU 1 299 " --> pdb=" O LYS 1 296 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU 1 300 " --> pdb=" O TYR 1 297 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL 1 304 " --> pdb=" O LEU 1 301 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA 1 305 " --> pdb=" O SER 1 302 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN 1 306 " --> pdb=" O ALA 1 303 " (cutoff:3.500A) Processing helix chain '1' and resid 311 through 315 Processing helix chain '1' and resid 324 through 326 No H-bonds generated for 'chain '1' and resid 324 through 326' Processing helix chain '1' and resid 331 through 333 No H-bonds generated for 'chain '1' and resid 331 through 333' Processing helix chain '1' and resid 339 through 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 Processing helix chain '1' and resid 393 through 420 removed outlier: 3.579A pdb=" N GLU 1 415 " --> pdb=" O ALA 1 411 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 426 through 431 Processing helix chain '1' and resid 436 through 443 Processing helix chain '1' and resid 447 through 459 removed outlier: 3.888A pdb=" N ARG 1 453 " --> pdb=" O ALA 1 449 " (cutoff:3.500A) Processing helix chain '1' and resid 464 through 478 Processing helix chain '1' and resid 480 through 482 No H-bonds generated for 'chain '1' and resid 480 through 482' Processing helix chain '1' and resid 486 through 489 No H-bonds generated for 'chain '1' and resid 486 through 489' Processing helix chain '1' and resid 491 through 515 removed outlier: 3.946A 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 578 through 587 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 593 through 605 Processing helix chain '2' and resid 8 through 19 Processing helix chain '2' and resid 26 through 37 Processing helix chain '2' and resid 46 through 56 Processing helix chain '2' and resid 63 through 76 Processing helix chain '2' and resid 81 through 93 removed outlier: 3.877A pdb=" N ALA 2 88 " --> pdb=" O VAL 2 84 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY 2 89 " --> pdb=" O ALA 2 85 " (cutoff:3.500A) Proline residue: 2 90 - end of helix Processing helix chain '2' and resid 100 through 113 removed outlier: 3.785A pdb=" N ALA 2 113 " --> pdb=" O ALA 2 109 " (cutoff:3.500A) Processing helix chain '2' and resid 118 through 130 Processing helix chain '2' and resid 137 through 149 Processing helix chain '2' and resid 156 through 167 removed outlier: 3.744A 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: 3.837A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS 2 198 " --> pdb=" O ASP 2 194 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N SER 2 199 " --> pdb=" O ALA 2 195 " (cutoff:3.500A) Processing helix chain '2' and resid 207 through 219 Processing helix chain '2' and resid 228 through 233 Processing helix chain '2' and resid 241 through 253 removed outlier: 4.233A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 259 through 275 removed outlier: 4.139A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL 2 269 " --> pdb=" O LEU 2 265 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 277 through 279 No H-bonds generated for 'chain '2' and resid 277 through 279' Processing helix chain '2' and resid 282 through 295 Processing helix chain '2' and resid 301 through 320 removed outlier: 4.516A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 340 Processing helix chain '2' and resid 346 through 353 Processing helix chain '2' and resid 397 through 407 Processing helix chain '2' and resid 418 through 421 No H-bonds generated for 'chain '2' and resid 418 through 421' Processing helix chain '2' and resid 428 through 441 removed outlier: 3.565A pdb=" N LYS 2 440 " --> pdb=" O ALA 2 436 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 88 removed outlier: 3.589A pdb=" N LYS 3 88 " --> pdb=" O THR 3 84 " (cutoff:3.500A) Processing helix chain '3' and resid 92 through 95 No H-bonds generated for 'chain '3' and resid 92 through 95' Processing helix chain '3' and resid 103 through 112 Processing helix chain '3' and resid 118 through 126 removed outlier: 4.670A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) Processing helix chain '3' and resid 129 through 134 removed outlier: 4.041A pdb=" N VAL 3 132 " --> pdb=" O LYS 3 129 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ALA 3 133 " --> pdb=" O PRO 3 130 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA 3 134 " --> pdb=" O LYS 3 131 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 129 through 134' Processing helix chain '3' and resid 137 through 149 Processing helix chain '3' and resid 155 through 167 removed outlier: 4.033A 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: 4.349A 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 229 removed outlier: 3.673A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 243 removed outlier: 3.741A pdb=" N ARG 3 242 " --> pdb=" O ALA 3 238 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY 3 243 " --> pdb=" O THR 3 239 " (cutoff:3.500A) Processing helix chain '3' and resid 246 through 249 No H-bonds generated for 'chain '3' and resid 246 through 249' Processing helix chain '3' and resid 254 through 271 removed outlier: 3.619A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 278 through 283 Processing helix chain '3' and resid 294 through 310 Processing helix chain '4' and resid 20 through 34 removed outlier: 3.985A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 68 removed outlier: 3.524A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 4.036A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (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: 3.786A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 175 removed outlier: 3.908A 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: 3.553A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 258 removed outlier: 3.542A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) Processing helix chain '4' and resid 263 through 284 Processing helix chain '5' and resid 8 through 29 Processing helix chain '5' and resid 31 through 58 removed outlier: 4.012A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.862A 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 73 through 80 Processing helix chain '5' and resid 88 through 105 removed outlier: 3.628A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA 5 105 " --> pdb=" O LYS 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 115 through 118 No H-bonds generated for 'chain '5' and resid 115 through 118' Processing helix chain '6' and resid 31 through 40 Processing helix chain '6' and resid 48 through 50 No H-bonds generated for 'chain '6' and resid 48 through 50' Processing helix chain '6' and resid 52 through 57 Processing helix chain '6' and resid 73 through 94 Processing helix chain '6' and resid 99 through 117 removed outlier: 3.817A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 130 Processing helix chain '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: 3.645A pdb=" N LEU 7 150 " --> pdb=" O PHE 7 147 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER 7 151 " --> pdb=" O ASP 7 148 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA 7 154 " --> pdb=" O SER 7 151 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER 7 155 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) removed outlier: 4.220A 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 79 removed outlier: 3.597A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA 8 79 " --> pdb=" O GLU 8 75 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 16 removed outlier: 3.851A pdb=" N LEU 9 7 " --> pdb=" O VAL 9 3 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY 9 8 " --> pdb=" O THR 9 4 " (cutoff:3.500A) Processing helix chain '9' and resid 36 through 54 removed outlier: 3.623A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 83 through 94 removed outlier: 3.930A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 67 removed outlier: 4.185A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 91 removed outlier: 3.866A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 98 through 125 removed outlier: 3.603A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 4.007A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 99 through 126 removed outlier: 3.959A pdb=" N LEU B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 89 removed outlier: 4.724A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 99 through 125 removed outlier: 3.809A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 91 removed outlier: 4.063A pdb=" N LYS D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 4.522A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 115 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D 124 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE D 126 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 89 removed outlier: 4.032A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 98 through 125 removed outlier: 3.627A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 91 removed outlier: 3.706A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 118 removed outlier: 4.565A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU F 104 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 removed outlier: 4.041A pdb=" N LEU F 125 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 91 removed outlier: 4.317A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 95 No H-bonds generated for 'chain 'G' and resid 93 through 95' Processing helix chain 'G' and resid 98 through 126 removed outlier: 3.621A pdb=" N LEU G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU G 125 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE G 126 " --> pdb=" O PHE G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 69 removed outlier: 4.301A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 91 removed outlier: 3.965A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 5.564A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN H 98 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA H 108 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL H 121 " --> pdb=" O LEU H 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 65 removed outlier: 3.708A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 91 removed outlier: 3.964A pdb=" N LEU I 85 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG I 91 " --> pdb=" O GLY I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 95 No H-bonds generated for 'chain 'I' and resid 93 through 95' Processing helix chain 'I' and resid 98 through 126 removed outlier: 4.275A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 89 removed outlier: 4.060A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 108 removed outlier: 3.522A pdb=" N ALA J 96 " --> pdb=" O PRO J 93 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LYS J 97 " --> pdb=" O ASN J 94 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU J 104 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA J 108 " --> pdb=" O LEU J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 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 164 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 197 Processing helix chain 'M' and resid 220 through 264 removed outlier: 3.850A pdb=" N LEU M 224 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA M 260 " --> pdb=" O GLY M 256 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 271 through 308 removed outlier: 3.955A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 62 removed outlier: 3.526A pdb=" N GLN P 59 " --> pdb=" O THR P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 78 removed outlier: 3.877A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 83 No H-bonds generated for 'chain 'P' and resid 80 through 83' Processing helix chain 'P' and resid 89 through 92 No H-bonds generated for 'chain 'P' and resid 89 through 92' Processing helix chain 'P' and resid 98 through 108 removed outlier: 3.535A pdb=" N THR P 102 " --> pdb=" O THR P 98 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 127 removed outlier: 3.527A pdb=" N PHE P 122 " --> pdb=" O THR P 118 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA P 126 " --> pdb=" O PHE P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 146 removed outlier: 4.226A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL P 137 " --> pdb=" O LEU P 134 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 174 Processing helix chain 'P' and resid 212 through 226 Processing helix chain 'Q' and resid 8 through 11 No H-bonds generated for 'chain 'Q' and resid 8 through 11' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.939A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 41 removed outlier: 4.620A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA Q 41 " --> pdb=" O ALA Q 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 37 Processing helix chain 'R' and resid 51 through 54 Processing helix chain 'R' and resid 159 through 167 removed outlier: 3.895A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 195 Processing helix chain 'S' and resid 40 through 78 removed outlier: 3.713A pdb=" N LYS S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 88 Processing helix chain 'S' and resid 115 through 130 Processing helix chain 'S' and resid 147 through 153 removed outlier: 4.048A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG S 152 " --> pdb=" O SER S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 184 Processing helix chain 'S' and resid 217 through 220 No H-bonds generated for 'chain 'S' and resid 217 through 220' Processing helix chain 'S' and resid 239 through 311 removed outlier: 3.588A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP S 245 " --> pdb=" O ASP S 241 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER S 277 " --> pdb=" O ALA S 273 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 75 removed outlier: 3.678A pdb=" N ILE T 67 " --> pdb=" O SER T 63 " (cutoff:3.500A) Proline residue: T 68 - end of helix removed outlier: 3.871A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 207 through 212 removed outlier: 3.666A pdb=" N ALA T 211 " --> pdb=" O LYS T 207 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 207 through 212' Processing helix chain 'T' and resid 231 through 245 removed outlier: 3.535A pdb=" N ALA T 235 " --> pdb=" O LYS T 231 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 279 Processing helix chain 'T' and resid 281 through 284 Processing helix chain 'T' and resid 296 through 315 Proline residue: T 303 - end of helix removed outlier: 3.721A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 4.136A pdb=" N VAL T 332 " --> pdb=" O LYS T 329 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN T 336 " --> pdb=" O ALA T 333 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET T 337 " --> pdb=" O TYR T 334 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER T 338 " --> pdb=" O ARG T 335 " (cutoff:3.500A) Processing helix chain 'T' and resid 352 through 364 removed outlier: 4.148A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU T 363 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 removed outlier: 3.539A pdb=" N ASN T 397 " --> pdb=" O TYR T 393 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL T 398 " --> pdb=" O ILE T 394 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER T 400 " --> pdb=" O THR T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 431 through 434 removed outlier: 4.185A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 431 through 434' Processing helix chain 'T' and resid 437 through 440 No H-bonds generated for 'chain 'T' and resid 437 through 440' Processing helix chain 'T' and resid 444 through 452 removed outlier: 3.522A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) Processing helix chain 'T' and resid 454 through 462 removed outlier: 3.682A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE T 462 " --> pdb=" O ALA T 458 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.583A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU T 480 " --> pdb=" O ARG T 476 " (cutoff:3.500A) Processing helix chain 'T' and resid 495 through 505 removed outlier: 3.772A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 514 through 520 removed outlier: 3.978A pdb=" N ILE T 517 " --> pdb=" O VAL T 514 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL T 518 " --> pdb=" O GLN T 515 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA T 520 " --> pdb=" O ILE T 517 " (cutoff:3.500A) Processing helix chain 'T' and resid 523 through 526 No H-bonds generated for 'chain 'T' and resid 523 through 526' Processing helix chain 'T' and resid 531 through 539 removed outlier: 3.622A pdb=" N LEU T 536 " --> pdb=" O VAL T 532 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA T 538 " --> pdb=" O LYS T 534 " (cutoff:3.500A) Processing helix chain 'T' and resid 544 through 555 removed outlier: 3.763A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS T 551 " --> pdb=" O ASP T 547 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU T 553 " --> pdb=" O HIS T 549 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG T 555 " --> pdb=" O LYS T 551 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 49 removed outlier: 3.923A pdb=" N ARG U 49 " --> pdb=" O ASP U 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 46 through 49' Processing helix chain 'U' and resid 59 through 63 Processing helix chain 'U' and resid 67 through 70 No H-bonds generated for 'chain 'U' and resid 67 through 70' Processing helix chain 'U' and resid 135 through 137 No H-bonds generated for 'chain 'U' and resid 135 through 137' Processing helix chain 'U' and resid 157 through 159 No H-bonds generated for 'chain 'U' and resid 157 through 159' Processing helix chain 'U' and resid 207 through 212 Processing helix chain 'U' and resid 231 through 248 removed outlier: 3.999A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLN U 248 " --> pdb=" O ASN U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 278 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 315 Proline residue: U 303 - end of helix removed outlier: 3.724A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 341 removed outlier: 3.666A pdb=" N LEU U 341 " --> pdb=" O MET U 337 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 362 removed outlier: 3.697A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 370 through 372 No H-bonds generated for 'chain 'U' and resid 370 through 372' Processing helix chain 'U' and resid 393 through 399 Processing helix chain 'U' and resid 410 through 414 Processing helix chain 'U' and resid 437 through 459 removed outlier: 3.619A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 484 removed outlier: 3.799A pdb=" N GLU U 482 " --> pdb=" O ALA U 478 " (cutoff:3.500A) Processing helix chain 'U' and resid 495 through 505 removed outlier: 4.035A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 527 removed outlier: 3.753A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 538 removed outlier: 4.248A pdb=" N LYS U 534 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 544 through 553 Processing helix chain 'V' and resid 45 through 48 Processing helix chain 'V' and resid 59 through 69 removed outlier: 3.717A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Proline residue: V 68 - end of helix Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 212 Processing helix chain 'V' and resid 231 through 246 Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.829A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 Processing helix chain 'V' and resid 354 through 364 removed outlier: 4.595A pdb=" N ARG V 364 " --> pdb=" O ARG V 360 " (cutoff:3.500A) Processing helix chain 'V' and resid 370 through 372 No H-bonds generated for 'chain 'V' and resid 370 through 372' Processing helix chain 'V' and resid 386 through 388 No H-bonds generated for 'chain 'V' and resid 386 through 388' Processing helix chain 'V' and resid 393 through 401 Processing helix chain 'V' and resid 411 through 414 No H-bonds generated for 'chain 'V' and resid 411 through 414' Processing helix chain 'V' and resid 431 through 434 removed outlier: 3.713A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 431 through 434' Processing helix chain 'V' and resid 440 through 455 removed outlier: 5.392A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 481 Processing helix chain 'V' and resid 494 through 506 Processing helix chain 'V' and resid 514 through 516 No H-bonds generated for 'chain 'V' and resid 514 through 516' Processing helix chain 'V' and resid 518 through 525 removed outlier: 4.247A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA V 523 " --> pdb=" O ALA V 519 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE V 525 " --> pdb=" O GLU V 521 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 539 removed outlier: 3.519A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 544 through 555 removed outlier: 3.648A pdb=" N LYS V 551 " --> pdb=" O ASP V 547 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG V 555 " --> pdb=" O LYS V 551 " (cutoff:3.500A) Processing helix chain 'X' and resid 165 through 169 Processing helix chain 'X' and resid 189 through 203 removed outlier: 4.682A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 227 Processing helix chain 'X' and resid 239 through 241 No H-bonds generated for 'chain 'X' and resid 239 through 241' Processing helix chain 'X' and resid 255 through 258 No H-bonds generated for 'chain 'X' and resid 255 through 258' Processing helix chain 'X' and resid 262 through 274 removed outlier: 3.810A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 288 through 297 Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.277A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 349 through 352 No H-bonds generated for 'chain 'X' and resid 349 through 352' Processing helix chain 'X' and resid 354 through 357 Processing helix chain 'X' and resid 366 through 371 removed outlier: 3.531A pdb=" N LEU X 371 " --> pdb=" O SER X 367 " (cutoff:3.500A) Processing helix chain 'X' and resid 389 through 420 removed outlier: 7.294A pdb=" N ALA X 394 " --> pdb=" O ASN X 390 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N GLU X 395 " --> pdb=" O VAL X 391 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N HIS X 396 " --> pdb=" O ILE X 392 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 424 No H-bonds generated for 'chain 'X' and resid 422 through 424' Processing helix chain 'X' and resid 427 through 442 Processing helix chain 'X' and resid 451 through 454 No H-bonds generated for 'chain 'X' and resid 451 through 454' Processing helix chain 'X' and resid 463 through 475 Processing helix chain 'X' and resid 484 through 486 No H-bonds generated for 'chain 'X' and resid 484 through 486' Processing helix chain 'X' and resid 492 through 507 Processing helix chain 'X' and resid 527 through 533 removed outlier: 4.736A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 169 Processing helix chain 'Y' and resid 189 through 200 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 4.715A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 274 removed outlier: 4.324A pdb=" N ARG Y 260 " --> pdb=" O GLY Y 256 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL Y 261 " --> pdb=" O ALA Y 257 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 297 removed outlier: 3.535A pdb=" N GLN Y 292 " --> pdb=" O ARG Y 289 " (cutoff:3.500A) Processing helix chain 'Y' and resid 314 through 324 removed outlier: 4.505A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 349 through 356 removed outlier: 3.860A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 389 through 392 No H-bonds generated for 'chain 'Y' and resid 389 through 392' Processing helix chain 'Y' and resid 394 through 420 removed outlier: 4.196A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA Y 418 " --> pdb=" O GLN Y 414 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 429 through 442 Processing helix chain 'Y' and resid 449 through 451 No H-bonds generated for 'chain 'Y' and resid 449 through 451' Processing helix chain 'Y' and resid 463 through 475 removed outlier: 3.642A pdb=" N THR Y 475 " --> pdb=" O GLN Y 471 " (cutoff:3.500A) Processing helix chain 'Y' and resid 483 through 485 No H-bonds generated for 'chain 'Y' and resid 483 through 485' Processing helix chain 'Y' and resid 492 through 508 removed outlier: 3.641A pdb=" N ASP Y 500 " --> pdb=" O LYS Y 496 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 510 through 512 No H-bonds generated for 'chain 'Y' and resid 510 through 512' Processing helix chain 'Y' and resid 527 through 532 Processing helix chain 'Y' and resid 545 through 554 removed outlier: 4.145A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 150 through 152 No H-bonds generated for 'chain 'Z' and resid 150 through 152' Processing helix chain 'Z' and resid 165 through 169 Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 217 through 229 Processing helix chain 'Z' and resid 239 through 241 No H-bonds generated for 'chain 'Z' and resid 239 through 241' Processing helix chain 'Z' and resid 255 through 258 No H-bonds generated for 'chain 'Z' and resid 255 through 258' Processing helix chain 'Z' and resid 261 through 274 removed outlier: 3.530A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 300 Processing helix chain 'Z' and resid 314 through 322 removed outlier: 3.871A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 355 Processing helix chain 'Z' and resid 366 through 370 Processing helix chain 'Z' and resid 394 through 417 removed outlier: 4.153A pdb=" N LEU Z 413 " --> pdb=" O ASP Z 409 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN Z 414 " --> pdb=" O TYR Z 410 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 427 through 442 removed outlier: 3.711A pdb=" N THR Z 432 " --> pdb=" O GLU Z 428 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 448 through 450 No H-bonds generated for 'chain 'Z' and resid 448 through 450' Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.541A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) Processing helix chain 'Z' and resid 495 through 510 removed outlier: 3.867A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER Z 508 " --> pdb=" O LYS Z 504 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG Z 509 " --> pdb=" O ASP Z 505 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LYS Z 510 " --> pdb=" O ILE Z 506 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 Processing sheet with id= A, first strand: chain '2' and resid 369 through 372 Processing sheet with id= B, first strand: chain '2' and resid 379 through 382 removed outlier: 6.373A pdb=" N ALA 2 414 " --> pdb=" O GLN 2 380 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL 2 382 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL 2 416 " --> pdb=" O VAL 2 382 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain '7' and resid 36 through 39 Processing sheet with id= D, first strand: chain 'P' and resid 155 through 158 removed outlier: 3.915A 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 96 through 100 removed outlier: 3.569A pdb=" N VAL R 90 " --> pdb=" O GLU R 117 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU R 117 " --> pdb=" O VAL R 90 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 107 through 111 removed outlier: 3.954A pdb=" N GLY R 132 " --> pdb=" O LEU R 111 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE R 135 " --> pdb=" O ASP R 143 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'S' and resid 158 through 162 removed outlier: 8.149A pdb=" N VAL S 139 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA S 161 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER S 141 " --> pdb=" O ALA S 161 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER S 189 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N VAL S 103 " --> pdb=" O SER S 189 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN S 191 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL S 105 " --> pdb=" O GLN S 191 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU S 193 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE S 194 " --> pdb=" O THR S 206 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS S 204 " --> pdb=" O LYS S 196 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'T' and resid 85 through 91 removed outlier: 6.737A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= K, first strand: chain 'T' and resid 404 through 407 removed outlier: 3.879A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 285 through 290 removed outlier: 9.123A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.425A 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: 6.687A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'U' and resid 109 through 111 Processing sheet with id= O, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= P, first strand: chain 'U' and resid 405 through 408 removed outlier: 6.783A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'U' and resid 285 through 290 removed outlier: 8.977A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'V' and resid 84 through 86 removed outlier: 3.672A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET V 118 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU V 120 " --> pdb=" O GLY V 128 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY V 128 " --> pdb=" O LEU V 120 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU V 122 " --> pdb=" O HIS V 126 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N HIS V 126 " --> pdb=" O LEU V 122 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR V 98 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL V 87 " --> pdb=" O TYR V 98 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= T, first strand: chain 'V' and resid 404 through 408 removed outlier: 3.804A pdb=" N LEU V 222 " --> pdb=" O GLY V 404 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.960A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'X' and resid 37 through 39 removed outlier: 6.646A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ARG X 51 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL X 40 " --> pdb=" O ARG X 51 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 110 through 113 Processing sheet with id= X, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.520A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= Z, first strand: chain 'Y' and resid 39 through 44 removed outlier: 6.405A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Y' and resid 360 through 362 removed outlier: 7.419A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL Y 280 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU Y 282 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA Y 338 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL Y 284 " --> pdb=" O ALA Y 338 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.614A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= AD, first strand: chain 'Z' and resid 360 through 363 removed outlier: 8.549A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL Z 284 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 559 through 561 2375 hydrogen bonds defined for protein. 6606 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: 16.58 Time building geometry restraints manager: 17.08 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: 15977 1.34 - 1.45: 8663 1.45 - 1.57: 29771 1.57 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54686 Sorted by residual: bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.24e+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 5.97e+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 5.69e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.46e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.45e+01 ... (remaining 54681 not shown) Histogram of bond angle deviations from ideal: 98.79 - 106.28: 1385 106.28 - 113.77: 31393 113.77 - 121.26: 28334 121.26 - 128.76: 12789 128.76 - 136.25: 260 Bond angle restraints: 74161 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 117.26 22.61 1.00e+00 1.00e+00 5.11e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 119.22 20.65 1.00e+00 1.00e+00 4.26e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 121.81 18.06 1.00e+00 1.00e+00 3.26e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 121.14 15.69 1.00e+00 1.00e+00 2.46e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 121.27 15.56 1.00e+00 1.00e+00 2.42e+02 ... (remaining 74156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 29928 17.88 - 35.75: 2524 35.75 - 53.63: 449 53.63 - 71.50: 79 71.50 - 89.38: 45 Dihedral angle restraints: 33025 sinusoidal: 12667 harmonic: 20358 Sorted by residual: dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -124.10 -55.90 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -126.27 -53.73 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA GLU V 348 " pdb=" C GLU V 348 " pdb=" N ALA V 349 " pdb=" CA ALA V 349 " ideal model delta harmonic sigma weight residual 180.00 126.83 53.17 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 33022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 7785 0.090 - 0.180: 863 0.180 - 0.270: 37 0.270 - 0.360: 2 0.360 - 0.450: 2 Chirality restraints: 8689 Sorted by residual: chirality pdb=" CB ILE U 67 " pdb=" CA ILE U 67 " pdb=" CG1 ILE U 67 " pdb=" CG2 ILE U 67 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" CB ILE 3 90 " pdb=" CA ILE 3 90 " pdb=" CG1 ILE 3 90 " pdb=" CG2 ILE 3 90 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CB ILE B 95 " pdb=" CA ILE B 95 " pdb=" CG1 ILE B 95 " pdb=" CG2 ILE B 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 8686 not shown) Planarity restraints: 9510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.87e-02 3.45e+01 pdb=" C ALA Z 503 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.037 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA 3 210 " 0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO 3 211 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO 3 211 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO 3 211 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA X 350 " -0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO X 351 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO X 351 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO X 351 " -0.045 5.00e-02 4.00e+02 ... (remaining 9507 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 894 2.66 - 3.22: 49322 3.22 - 3.78: 86531 3.78 - 4.34: 118418 4.34 - 4.90: 192807 Nonbonded interactions: 447972 Sorted by model distance: nonbonded pdb=" O3B ADP Y 601 " pdb="MG MG Y 602 " model vdw 2.103 2.170 nonbonded pdb=" O2B ATP V1001 " pdb="MG MG V1002 " model vdw 2.104 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.114 2.170 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.117 2.170 nonbonded pdb=" O2B ATP U1001 " pdb="MG MG U1002 " model vdw 2.118 2.170 ... (remaining 447967 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.730 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: 0.060 Extract box with map and model: 23.380 Check model and map are aligned: 0.590 Set scattering table: 0.380 Process input model: 112.490 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 0.081 54686 Z= 0.410 Angle : 0.909 22.606 74161 Z= 0.528 Chirality : 0.056 0.450 8689 Planarity : 0.007 0.082 9510 Dihedral : 14.127 89.380 19939 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.93 % Favored : 94.86 % Rotamer: Outliers : 0.44 % Allowed : 7.30 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.08), residues: 7038 helix: -3.12 (0.06), residues: 3812 sheet: -2.13 (0.20), residues: 578 loop : -2.39 (0.10), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP Z 141 HIS 0.014 0.002 HIS S 250 PHE 0.027 0.002 PHE M 231 TYR 0.032 0.002 TYR X 340 ARG 0.007 0.001 ARG U 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1390 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1365 time to evaluate : 4.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 341 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7557 (mt-10) REVERT: 1 423 ASN cc_start: 0.7914 (p0) cc_final: 0.7691 (p0) REVERT: 1 456 LYS cc_start: 0.8780 (tmtt) cc_final: 0.8497 (ttmm) REVERT: 1 586 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7088 (mm-30) REVERT: 1 589 SER cc_start: 0.8882 (p) cc_final: 0.8681 (p) REVERT: 2 78 VAL cc_start: 0.8177 (OUTLIER) cc_final: 0.7860 (t) REVERT: 3 205 CYS cc_start: 0.8540 (m) cc_final: 0.8259 (m) REVERT: 3 297 LEU cc_start: 0.7395 (tt) cc_final: 0.7194 (tt) REVERT: 4 61 GLN cc_start: 0.8685 (mt0) cc_final: 0.8461 (mt0) REVERT: 5 63 ASP cc_start: 0.7506 (p0) cc_final: 0.7242 (p0) REVERT: 5 104 ASP cc_start: 0.7449 (t0) cc_final: 0.6480 (t0) REVERT: 5 112 ARG cc_start: 0.8032 (ptt180) cc_final: 0.7313 (ptt-90) REVERT: 6 80 PHE cc_start: 0.7263 (t80) cc_final: 0.6750 (m-10) REVERT: 7 117 ASP cc_start: 0.8158 (p0) cc_final: 0.7863 (p0) REVERT: 8 62 ASP cc_start: 0.8530 (t70) cc_final: 0.8320 (t0) REVERT: 8 69 LYS cc_start: 0.8902 (mttt) cc_final: 0.7424 (tmtt) REVERT: 9 35 GLN cc_start: 0.6710 (mm110) cc_final: 0.6215 (mt0) REVERT: 9 89 MET cc_start: 0.7173 (mtp) cc_final: 0.5224 (mtt) REVERT: B 97 LYS cc_start: 0.6568 (mmtt) cc_final: 0.5721 (mmmt) REVERT: B 122 PHE cc_start: 0.7904 (m-10) cc_final: 0.7598 (m-80) REVERT: C 68 THR cc_start: 0.7977 (p) cc_final: 0.7645 (m) REVERT: C 97 LYS cc_start: 0.7136 (mptt) cc_final: 0.6734 (mptt) REVERT: D 81 MET cc_start: 0.7603 (ttp) cc_final: 0.7069 (tmm) REVERT: D 82 PHE cc_start: 0.7324 (m-80) cc_final: 0.6981 (m-10) REVERT: D 85 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6982 (tp) REVERT: E 86 ILE cc_start: 0.6705 (mt) cc_final: 0.6331 (mt) REVERT: I 95 ILE cc_start: 0.7316 (mm) cc_final: 0.6458 (mm) REVERT: J 98 GLN cc_start: 0.7826 (tt0) cc_final: 0.7617 (tt0) REVERT: M 227 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8138 (tp) REVERT: M 311 ASN cc_start: 0.9073 (t0) cc_final: 0.8196 (t0) REVERT: M 324 LYS cc_start: 0.7711 (ttpt) cc_final: 0.7279 (mttp) REVERT: P 101 ARG cc_start: 0.7989 (ttp-110) cc_final: 0.7211 (ttp-110) REVERT: Q 19 TYR cc_start: 0.7570 (t80) cc_final: 0.6944 (t80) REVERT: R 54 TYR cc_start: 0.6123 (m-80) cc_final: 0.5896 (m-10) REVERT: R 70 PHE cc_start: 0.5756 (p90) cc_final: 0.5270 (p90) REVERT: S 41 GLN cc_start: 0.6497 (mm-40) cc_final: 0.6249 (tm-30) REVERT: S 291 ASP cc_start: 0.7986 (t70) cc_final: 0.7670 (t0) REVERT: T 322 ILE cc_start: 0.8653 (tp) cc_final: 0.8308 (tt) REVERT: U 337 MET cc_start: 0.8147 (ttp) cc_final: 0.7801 (ttp) REVERT: V 213 VAL cc_start: 0.9115 (m) cc_final: 0.8858 (p) REVERT: V 456 VAL cc_start: 0.8194 (m) cc_final: 0.7645 (t) REVERT: Y 80 MET cc_start: 0.7848 (mmm) cc_final: 0.7587 (mmm) REVERT: Y 151 THR cc_start: 0.7380 (p) cc_final: 0.7122 (t) REVERT: Y 409 ASP cc_start: 0.8506 (t0) cc_final: 0.7900 (t0) REVERT: Y 535 LYS cc_start: 0.5899 (tmtt) cc_final: 0.5525 (mmtm) outliers start: 25 outliers final: 6 residues processed: 1383 average time/residue: 0.5467 time to fit residues: 1241.1104 Evaluate side-chains 722 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 713 time to evaluate : 4.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 78 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain M residue 227 ILE Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain U residue 316 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 328 THR Chi-restraints excluded: chain Y residue 489 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 0.0270 chunk 529 optimal weight: 9.9990 chunk 293 optimal weight: 0.9980 chunk 180 optimal weight: 10.0000 chunk 356 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 547 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 332 optimal weight: 7.9990 chunk 407 optimal weight: 6.9990 chunk 633 optimal weight: 0.7980 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 0 48 ASN 1 285 GLN 1 298 GLN 1 313 GLN 1 316 ASN 1 365 GLN ** 1 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 582 GLN 1 587 ASN 1 590 HIS 1 606 ASN 2 68 ASN 2 122 ASN 2 243 GLN 2 289 HIS 2 409 GLN 3 229 ASN 4 135 ASN 4 240 GLN 5 9 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 60 GLN ** 7 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS A 87 ASN A 98 GLN H 98 GLN M 120 GLN M 163 ASN P 223 ASN Q 29 ASN R 38 ASN R 66 HIS ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 257 ASN S 262 ASN S 293 ASN S 297 GLN T 64 GLN ** T 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 139 HIS T 228 GLN T 241 HIS T 386 GLN U 134 ASN U 169 GLN ** U 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 248 GLN ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN U 486 GLN U 488 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 152 ASN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS V 271 GLN V 278 GLN V 397 ASN V 497 GLN X 144 HIS X 198 ASN X 199 ASN X 241 ASN X 250 GLN X 278 GLN X 448 GLN ** Y 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 174 GLN Y 221 ASN Y 241 ASN Z 42 GLN ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 144 HIS Z 153 GLN Z 198 ASN Z 199 ASN Z 241 ASN Z 250 GLN Z 278 GLN ** Z 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 322 GLN Z 337 GLN Z 440 GLN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 54686 Z= 0.211 Angle : 0.631 14.078 74161 Z= 0.323 Chirality : 0.043 0.204 8689 Planarity : 0.005 0.058 9510 Dihedral : 6.359 87.148 7683 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.09 % Favored : 95.75 % Rotamer: Outliers : 2.81 % Allowed : 14.14 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.09), residues: 7038 helix: -1.48 (0.07), residues: 3815 sheet: -1.78 (0.20), residues: 593 loop : -1.78 (0.11), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 141 HIS 0.007 0.001 HIS S 250 PHE 0.024 0.002 PHE U 508 TYR 0.027 0.001 TYR X 340 ARG 0.005 0.000 ARG Z 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 797 time to evaluate : 4.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 423 ASN cc_start: 0.7971 (p0) cc_final: 0.7713 (p0) REVERT: 1 441 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7530 (t80) REVERT: 1 456 LYS cc_start: 0.8773 (tmtt) cc_final: 0.8529 (ttmm) REVERT: 1 589 SER cc_start: 0.8814 (p) cc_final: 0.8565 (p) REVERT: 3 297 LEU cc_start: 0.7649 (tt) cc_final: 0.7286 (tt) REVERT: 4 57 TYR cc_start: 0.9092 (m-80) cc_final: 0.8700 (m-80) REVERT: 5 51 TYR cc_start: 0.8685 (t80) cc_final: 0.8465 (t80) REVERT: 5 95 MET cc_start: 0.8991 (mmm) cc_final: 0.8732 (mmt) REVERT: 5 104 ASP cc_start: 0.7379 (t0) cc_final: 0.6525 (t0) REVERT: 5 109 GLN cc_start: 0.8304 (mp-120) cc_final: 0.8091 (mt0) REVERT: 5 112 ARG cc_start: 0.7951 (ptt180) cc_final: 0.7265 (ptt-90) REVERT: 6 80 PHE cc_start: 0.7281 (t80) cc_final: 0.6756 (m-10) REVERT: 7 87 SER cc_start: 0.9347 (p) cc_final: 0.8778 (m) REVERT: 7 117 ASP cc_start: 0.8186 (p0) cc_final: 0.7883 (p0) REVERT: 8 69 LYS cc_start: 0.8855 (mttt) cc_final: 0.7444 (tmtt) REVERT: 9 35 GLN cc_start: 0.6487 (mm110) cc_final: 0.6109 (mt0) REVERT: B 78 LEU cc_start: 0.9033 (mt) cc_final: 0.8793 (mt) REVERT: B 97 LYS cc_start: 0.6758 (mmtt) cc_final: 0.5691 (mmmt) REVERT: B 122 PHE cc_start: 0.7940 (m-10) cc_final: 0.7628 (m-80) REVERT: C 61 MET cc_start: 0.7152 (mmm) cc_final: 0.6741 (mmm) REVERT: C 68 THR cc_start: 0.7944 (p) cc_final: 0.7539 (m) REVERT: C 97 LYS cc_start: 0.6467 (mptt) cc_final: 0.6123 (mmmt) REVERT: D 81 MET cc_start: 0.7541 (ttp) cc_final: 0.7245 (tmm) REVERT: E 56 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6001 (pt) REVERT: G 66 CYS cc_start: 0.7842 (m) cc_final: 0.7166 (t) REVERT: I 95 ILE cc_start: 0.7232 (mm) cc_final: 0.6683 (mm) REVERT: M 178 LEU cc_start: 0.8483 (tp) cc_final: 0.8118 (tp) REVERT: M 311 ASN cc_start: 0.8887 (t0) cc_final: 0.8117 (t0) REVERT: M 324 LYS cc_start: 0.7625 (ttpt) cc_final: 0.7153 (mttp) REVERT: P 141 TYR cc_start: 0.8257 (t80) cc_final: 0.8037 (t80) REVERT: P 185 VAL cc_start: 0.7612 (OUTLIER) cc_final: 0.7405 (p) REVERT: Q 19 TYR cc_start: 0.7665 (t80) cc_final: 0.7052 (t80) REVERT: Q 65 LEU cc_start: 0.3198 (mp) cc_final: 0.2815 (tp) REVERT: R 54 TYR cc_start: 0.6336 (m-80) cc_final: 0.5968 (m-10) REVERT: S 41 GLN cc_start: 0.6480 (mm-40) cc_final: 0.5895 (tm-30) REVERT: S 51 LYS cc_start: 0.7203 (mtpp) cc_final: 0.6937 (mtpp) REVERT: S 69 LYS cc_start: 0.7063 (ptpp) cc_final: 0.6760 (tptp) REVERT: T 322 ILE cc_start: 0.8741 (tp) cc_final: 0.8365 (tt) REVERT: T 357 LEU cc_start: 0.9080 (tp) cc_final: 0.8795 (tt) REVERT: U 186 GLU cc_start: 0.7923 (tp30) cc_final: 0.7637 (tp30) REVERT: U 337 MET cc_start: 0.8127 (ttp) cc_final: 0.7859 (ttp) REVERT: U 439 MET cc_start: 0.6620 (tpp) cc_final: 0.6331 (tpp) REVERT: U 454 ARG cc_start: 0.7431 (tpp-160) cc_final: 0.7193 (mmm160) REVERT: V 213 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8899 (p) REVERT: X 552 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: Y 80 MET cc_start: 0.7836 (mmm) cc_final: 0.7426 (mmm) REVERT: Y 386 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6845 (tpt) REVERT: Y 409 ASP cc_start: 0.8623 (t0) cc_final: 0.8006 (t0) REVERT: Y 488 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6484 (mmp) REVERT: Y 535 LYS cc_start: 0.5941 (tmtt) cc_final: 0.5517 (mmtm) REVERT: Z 289 ARG cc_start: 0.7744 (mtt90) cc_final: 0.6785 (mtm180) REVERT: Z 386 MET cc_start: 0.7159 (mmm) cc_final: 0.6706 (ttm) outliers start: 158 outliers final: 89 residues processed: 906 average time/residue: 0.4739 time to fit residues: 737.5278 Evaluate side-chains 773 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 677 time to evaluate : 4.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 VAL Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 441 PHE Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 278 ASP Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 3 residue 119 ASP Chi-restraints excluded: chain 3 residue 126 GLU Chi-restraints excluded: chain 3 residue 161 ILE Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 4 residue 116 SER Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 229 ILE Chi-restraints excluded: chain 4 residue 282 VAL Chi-restraints excluded: chain 5 residue 34 ILE Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 107 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 127 PHE Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 180 GLU Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 525 ILE Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 159 THR Chi-restraints excluded: chain U residue 316 THR Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 397 ASN Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 311 GLN Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain X residue 493 LYS Chi-restraints excluded: chain X residue 552 GLU Chi-restraints excluded: chain X residue 566 LYS Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 328 THR Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 488 MET Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 493 LYS Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain Z residue 233 ILE Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 527 optimal weight: 8.9990 chunk 431 optimal weight: 10.0000 chunk 174 optimal weight: 0.0470 chunk 635 optimal weight: 30.0000 chunk 685 optimal weight: 1.9990 chunk 565 optimal weight: 1.9990 chunk 629 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 509 optimal weight: 4.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 313 GLN ** 1 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 189 HIS 4 68 HIS 7 86 HIS ** 7 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS A 98 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN M 295 GLN Q 29 ASN R 83 GLN ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 185 HIS S 219 GLN U 241 HIS U 242 GLN ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 452 GLN U 486 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 248 GLN V 358 HIS ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 HIS Y 132 GLN Y 153 GLN ** Y 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 398 ASN ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 278 GLN Z 311 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 54686 Z= 0.270 Angle : 0.627 11.609 74161 Z= 0.319 Chirality : 0.044 0.238 8689 Planarity : 0.004 0.048 9510 Dihedral : 6.219 89.228 7677 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.66 % Favored : 95.18 % Rotamer: Outliers : 3.64 % Allowed : 16.46 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.10), residues: 7038 helix: -0.81 (0.08), residues: 3815 sheet: -1.44 (0.21), residues: 592 loop : -1.47 (0.12), residues: 2631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 4 206 HIS 0.014 0.001 HIS V 241 PHE 0.025 0.002 PHE E 107 TYR 0.035 0.002 TYR G 102 ARG 0.005 0.000 ARG Y 401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 720 time to evaluate : 4.500 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: 1 261 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8386 (mp) REVERT: 1 441 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7570 (t80) REVERT: 1 456 LYS cc_start: 0.8692 (tmtt) cc_final: 0.8488 (ttmm) REVERT: 3 115 PHE cc_start: 0.7625 (t80) cc_final: 0.7190 (t80) REVERT: 4 57 TYR cc_start: 0.9102 (m-80) cc_final: 0.8765 (m-80) REVERT: 5 63 ASP cc_start: 0.7754 (p0) cc_final: 0.7544 (p0) REVERT: 5 95 MET cc_start: 0.9045 (mmm) cc_final: 0.8698 (mmt) REVERT: 5 104 ASP cc_start: 0.7426 (t0) cc_final: 0.6463 (t0) REVERT: 5 109 GLN cc_start: 0.8349 (mp-120) cc_final: 0.8115 (mt0) REVERT: 5 112 ARG cc_start: 0.7949 (ptt180) cc_final: 0.7288 (ptt-90) REVERT: 6 80 PHE cc_start: 0.7345 (t80) cc_final: 0.6782 (m-10) REVERT: 7 38 ASN cc_start: 0.6613 (OUTLIER) cc_final: 0.6380 (p0) REVERT: 8 69 LYS cc_start: 0.8885 (mttt) cc_final: 0.7429 (tmtt) REVERT: 9 35 GLN cc_start: 0.6524 (mm110) cc_final: 0.6200 (mt0) REVERT: B 78 LEU cc_start: 0.9032 (mt) cc_final: 0.8685 (mt) REVERT: B 97 LYS cc_start: 0.6791 (mmtt) cc_final: 0.5849 (mmmt) REVERT: C 61 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6393 (mmm) REVERT: C 68 THR cc_start: 0.8128 (p) cc_final: 0.7767 (m) REVERT: E 56 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6336 (pt) REVERT: F 116 PHE cc_start: 0.7447 (m-10) cc_final: 0.7161 (m-80) REVERT: I 95 ILE cc_start: 0.7474 (mm) cc_final: 0.7012 (mm) REVERT: J 95 ILE cc_start: 0.6938 (mp) cc_final: 0.6613 (mp) REVERT: J 122 PHE cc_start: 0.6441 (m-80) cc_final: 0.6085 (m-80) REVERT: M 110 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9190 (tt) REVERT: M 178 LEU cc_start: 0.8536 (tp) cc_final: 0.8174 (tp) REVERT: M 324 LYS cc_start: 0.7718 (ttpt) cc_final: 0.7276 (mttp) REVERT: Q 19 TYR cc_start: 0.7734 (t80) cc_final: 0.7039 (t80) REVERT: Q 42 ARG cc_start: 0.6420 (ptp90) cc_final: 0.6193 (ttp80) REVERT: R 54 TYR cc_start: 0.6553 (m-80) cc_final: 0.6139 (m-10) REVERT: S 41 GLN cc_start: 0.6495 (mm-40) cc_final: 0.5948 (tm-30) REVERT: S 51 LYS cc_start: 0.7178 (mtpp) cc_final: 0.6868 (mtpp) REVERT: S 238 GLU cc_start: 0.7693 (pm20) cc_final: 0.7256 (pt0) REVERT: T 322 ILE cc_start: 0.8824 (tp) cc_final: 0.8458 (tt) REVERT: U 213 VAL cc_start: 0.7855 (OUTLIER) cc_final: 0.7557 (m) REVERT: U 439 MET cc_start: 0.6832 (tpp) cc_final: 0.6577 (tpp) REVERT: V 74 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: X 401 ARG cc_start: 0.6993 (mmt180) cc_final: 0.6416 (mmt180) REVERT: X 424 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7125 (mm-30) REVERT: X 535 LYS cc_start: 0.7416 (mtmm) cc_final: 0.7182 (tttm) REVERT: Y 80 MET cc_start: 0.7825 (mmm) cc_final: 0.7411 (mmm) REVERT: Y 355 PHE cc_start: 0.7833 (m-80) cc_final: 0.7578 (m-10) REVERT: Y 409 ASP cc_start: 0.8680 (t0) cc_final: 0.8090 (t0) REVERT: Y 535 LYS cc_start: 0.6169 (tmtt) cc_final: 0.5455 (mmtm) REVERT: Z 289 ARG cc_start: 0.7820 (mtt90) cc_final: 0.6840 (mtm180) REVERT: Z 386 MET cc_start: 0.7210 (mmm) cc_final: 0.7005 (tpp) outliers start: 205 outliers final: 127 residues processed: 866 average time/residue: 0.4814 time to fit residues: 716.3140 Evaluate side-chains 778 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 642 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 VAL Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 313 GLN Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 424 VAL Chi-restraints excluded: chain 1 residue 441 PHE Chi-restraints excluded: chain 1 residue 524 THR Chi-restraints excluded: chain 1 residue 595 LEU Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 2 residue 223 LYS Chi-restraints excluded: chain 2 residue 278 ASP Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 3 residue 119 ASP Chi-restraints excluded: chain 3 residue 126 GLU Chi-restraints excluded: chain 3 residue 161 ILE Chi-restraints excluded: chain 3 residue 187 PHE Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 229 ILE Chi-restraints excluded: chain 4 residue 282 VAL Chi-restraints excluded: chain 5 residue 34 ILE Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 107 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 6 residue 147 SER Chi-restraints excluded: chain 7 residue 38 ASN Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 184 ASN Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 78 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 127 PHE Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 169 GLN Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 316 THR Chi-restraints excluded: chain U residue 426 SER Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 424 GLU Chi-restraints excluded: chain X residue 439 ILE Chi-restraints excluded: chain X residue 493 LYS Chi-restraints excluded: chain X residue 558 THR Chi-restraints excluded: chain X residue 566 LYS Chi-restraints excluded: chain X residue 573 LYS Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 252 ASN Chi-restraints excluded: chain Y residue 263 LEU Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 328 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 493 LYS Chi-restraints excluded: chain Z residue 80 MET Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain Z residue 233 ILE Chi-restraints excluded: chain Z residue 297 VAL Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 407 LEU Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 491 ASP Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 3.9990 chunk 477 optimal weight: 5.9990 chunk 329 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 303 optimal weight: 4.9990 chunk 426 optimal weight: 1.9990 chunk 637 optimal weight: 0.0980 chunk 674 optimal weight: 9.9990 chunk 332 optimal weight: 7.9990 chunk 603 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 81 ASN 1 313 GLN 1 423 ASN ** 1 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 107 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 98 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS F 98 GLN G 98 GLN Q 29 ASN R 83 GLN ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 219 GLN S 293 ASN ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 549 HIS ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 386 GLN V 397 ASN ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 250 GLN ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 278 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54686 Z= 0.199 Angle : 0.582 10.703 74161 Z= 0.293 Chirality : 0.042 0.211 8689 Planarity : 0.004 0.044 9510 Dihedral : 5.944 86.847 7674 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.18 % Favored : 95.68 % Rotamer: Outliers : 3.39 % Allowed : 18.06 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.10), residues: 7038 helix: -0.37 (0.08), residues: 3815 sheet: -1.16 (0.22), residues: 555 loop : -1.30 (0.12), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 9 73 HIS 0.011 0.001 HIS V 241 PHE 0.028 0.001 PHE V 459 TYR 0.024 0.001 TYR G 102 ARG 0.007 0.000 ARG Z 401 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 729 time to evaluate : 4.489 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: 1 261 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8341 (mp) REVERT: 1 441 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7560 (t80) REVERT: 2 108 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7603 (tm-30) REVERT: 3 115 PHE cc_start: 0.7550 (t80) cc_final: 0.7098 (t80) REVERT: 4 57 TYR cc_start: 0.9116 (m-80) cc_final: 0.8802 (m-80) REVERT: 5 63 ASP cc_start: 0.7760 (p0) cc_final: 0.7484 (p0) REVERT: 5 95 MET cc_start: 0.9045 (mmm) cc_final: 0.8552 (mmt) REVERT: 5 104 ASP cc_start: 0.7370 (t0) cc_final: 0.6434 (t0) REVERT: 5 109 GLN cc_start: 0.8346 (mp-120) cc_final: 0.8046 (mt0) REVERT: 5 112 ARG cc_start: 0.7919 (ptt180) cc_final: 0.7250 (ptt-90) REVERT: 6 80 PHE cc_start: 0.7383 (t80) cc_final: 0.6790 (m-10) REVERT: 7 38 ASN cc_start: 0.6778 (OUTLIER) cc_final: 0.6530 (p0) REVERT: 7 117 ASP cc_start: 0.8037 (p0) cc_final: 0.7700 (t0) REVERT: 8 69 LYS cc_start: 0.8879 (mttt) cc_final: 0.7460 (tmtt) REVERT: 9 17 ASP cc_start: 0.5990 (p0) cc_final: 0.5735 (p0) REVERT: 9 30 LEU cc_start: 0.7454 (tt) cc_final: 0.6308 (mp) REVERT: 9 35 GLN cc_start: 0.6556 (mm110) cc_final: 0.6239 (mt0) REVERT: B 78 LEU cc_start: 0.8936 (mt) cc_final: 0.8644 (mt) REVERT: B 97 LYS cc_start: 0.6688 (mmtt) cc_final: 0.5798 (mmmt) REVERT: B 122 PHE cc_start: 0.7884 (m-80) cc_final: 0.7650 (m-80) REVERT: C 61 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6382 (mmm) REVERT: C 68 THR cc_start: 0.8142 (p) cc_final: 0.7821 (m) REVERT: C 97 LYS cc_start: 0.6747 (mptt) cc_final: 0.6351 (mmtt) REVERT: E 56 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6371 (pt) REVERT: F 116 PHE cc_start: 0.7390 (m-10) cc_final: 0.7127 (m-80) REVERT: I 61 MET cc_start: 0.4828 (mmt) cc_final: 0.4627 (mmm) REVERT: I 95 ILE cc_start: 0.7269 (mm) cc_final: 0.6870 (mm) REVERT: J 122 PHE cc_start: 0.6417 (m-80) cc_final: 0.6054 (m-80) REVERT: M 311 ASN cc_start: 0.8883 (t0) cc_final: 0.8204 (t0) REVERT: M 324 LYS cc_start: 0.7657 (ttpt) cc_final: 0.7155 (mttp) REVERT: P 135 LEU cc_start: 0.8452 (mm) cc_final: 0.8171 (mp) REVERT: P 182 PHE cc_start: 0.7790 (m-80) cc_final: 0.7395 (m-80) REVERT: Q 19 TYR cc_start: 0.7663 (t80) cc_final: 0.6902 (t80) REVERT: Q 32 LYS cc_start: 0.6039 (tppt) cc_final: 0.5450 (mttp) REVERT: R 54 TYR cc_start: 0.6420 (m-80) cc_final: 0.6109 (m-10) REVERT: S 41 GLN cc_start: 0.6516 (mm-40) cc_final: 0.5845 (tm-30) REVERT: S 51 LYS cc_start: 0.7158 (mtpp) cc_final: 0.6857 (mtpp) REVERT: S 238 GLU cc_start: 0.7683 (pm20) cc_final: 0.7051 (pt0) REVERT: T 322 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8489 (tt) REVERT: T 398 VAL cc_start: 0.9232 (m) cc_final: 0.8926 (t) REVERT: U 213 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7508 (m) REVERT: U 353 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7721 (p0) REVERT: U 439 MET cc_start: 0.6836 (tpp) cc_final: 0.6619 (tpp) REVERT: X 424 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.7074 (mm-30) REVERT: X 535 LYS cc_start: 0.7767 (mtmm) cc_final: 0.7313 (tttm) REVERT: Y 80 MET cc_start: 0.7847 (mmm) cc_final: 0.7416 (mmm) REVERT: Y 355 PHE cc_start: 0.7920 (m-80) cc_final: 0.7636 (m-10) REVERT: Y 409 ASP cc_start: 0.8627 (t0) cc_final: 0.8095 (t0) REVERT: Y 535 LYS cc_start: 0.6251 (tmtt) cc_final: 0.5495 (mppt) outliers start: 191 outliers final: 122 residues processed: 864 average time/residue: 0.4776 time to fit residues: 712.2271 Evaluate side-chains 773 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 642 time to evaluate : 4.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 VAL Chi-restraints excluded: chain 1 residue 61 MET Chi-restraints excluded: chain 1 residue 107 VAL Chi-restraints excluded: chain 1 residue 123 ILE Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 293 ILE Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 423 ASN Chi-restraints excluded: chain 1 residue 441 PHE Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 2 residue 278 ASP Chi-restraints excluded: chain 2 residue 390 THR Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 3 residue 119 ASP Chi-restraints excluded: chain 3 residue 126 GLU Chi-restraints excluded: chain 3 residue 161 ILE Chi-restraints excluded: chain 3 residue 187 PHE Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 229 ILE Chi-restraints excluded: chain 4 residue 282 VAL Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 107 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 38 ASN Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 127 PHE Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 315 MET Chi-restraints excluded: chain T residue 224 ILE Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 400 SER Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 169 GLN Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 316 THR Chi-restraints excluded: chain U residue 353 ASP Chi-restraints excluded: chain U residue 359 SER Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 138 ILE Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 386 GLN Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 223 LEU Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 424 GLU Chi-restraints excluded: chain X residue 493 LYS Chi-restraints excluded: chain X residue 566 LYS Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 252 ASN Chi-restraints excluded: chain Y residue 263 LEU Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 328 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 493 LYS Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Z residue 80 MET Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain Z residue 233 ILE Chi-restraints excluded: chain Z residue 297 VAL Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 407 LEU Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 491 ASP Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 0.0870 chunk 382 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 502 optimal weight: 6.9990 chunk 278 optimal weight: 20.0000 chunk 575 optimal weight: 0.9990 chunk 466 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 344 optimal weight: 4.9990 chunk 605 optimal weight: 0.6980 chunk 170 optimal weight: 10.0000 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 111 GLN 5 107 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS J 98 GLN P 148 HIS Q 29 ASN R 83 GLN ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 248 GLN ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 54686 Z= 0.238 Angle : 0.599 12.487 74161 Z= 0.301 Chirality : 0.043 0.204 8689 Planarity : 0.004 0.044 9510 Dihedral : 5.883 88.803 7674 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.63 % Favored : 95.23 % Rotamer: Outliers : 4.00 % Allowed : 18.56 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.10), residues: 7038 helix: -0.19 (0.08), residues: 3829 sheet: -1.04 (0.22), residues: 581 loop : -1.17 (0.12), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 4 206 HIS 0.011 0.001 HIS V 241 PHE 0.031 0.001 PHE Y 447 TYR 0.023 0.001 TYR 4 211 ARG 0.008 0.000 ARG Z 401 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 667 time to evaluate : 4.511 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: 1 261 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8346 (mp) REVERT: 1 441 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7575 (t80) REVERT: 2 74 ASN cc_start: 0.8332 (t0) cc_final: 0.7742 (m-40) REVERT: 2 108 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7341 (tm-30) REVERT: 5 63 ASP cc_start: 0.7772 (p0) cc_final: 0.7539 (p0) REVERT: 5 95 MET cc_start: 0.9049 (mmm) cc_final: 0.8620 (mmt) REVERT: 5 104 ASP cc_start: 0.7402 (t0) cc_final: 0.6446 (t0) REVERT: 5 109 GLN cc_start: 0.8334 (mp-120) cc_final: 0.8078 (mt0) REVERT: 5 112 ARG cc_start: 0.7934 (ptt180) cc_final: 0.7269 (ptt-90) REVERT: 6 80 PHE cc_start: 0.7474 (t80) cc_final: 0.6796 (m-10) REVERT: 7 38 ASN cc_start: 0.6801 (OUTLIER) cc_final: 0.6553 (p0) REVERT: 8 69 LYS cc_start: 0.8883 (mttt) cc_final: 0.7451 (tmtt) REVERT: 8 85 THR cc_start: 0.7665 (m) cc_final: 0.7278 (p) REVERT: 9 30 LEU cc_start: 0.7491 (tt) cc_final: 0.6328 (mp) REVERT: 9 35 GLN cc_start: 0.6525 (mm110) cc_final: 0.6235 (mt0) REVERT: B 97 LYS cc_start: 0.6762 (mmtt) cc_final: 0.5952 (mmmt) REVERT: B 122 PHE cc_start: 0.7861 (m-80) cc_final: 0.7533 (m-80) REVERT: C 61 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6258 (mmm) REVERT: C 68 THR cc_start: 0.8189 (p) cc_final: 0.7894 (m) REVERT: C 97 LYS cc_start: 0.6700 (mptt) cc_final: 0.6328 (mmtt) REVERT: E 56 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6435 (pt) REVERT: F 116 PHE cc_start: 0.7467 (m-10) cc_final: 0.7232 (m-80) REVERT: G 113 ILE cc_start: 0.6525 (OUTLIER) cc_final: 0.6075 (tp) REVERT: I 95 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7014 (mm) REVERT: J 122 PHE cc_start: 0.6382 (m-80) cc_final: 0.6020 (m-80) REVERT: M 110 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.8975 (tt) REVERT: M 324 LYS cc_start: 0.7712 (ttpt) cc_final: 0.7242 (mttp) REVERT: Q 19 TYR cc_start: 0.7622 (t80) cc_final: 0.6811 (t80) REVERT: Q 32 LYS cc_start: 0.6103 (tppt) cc_final: 0.5430 (mttp) REVERT: Q 49 GLN cc_start: 0.8300 (pm20) cc_final: 0.8082 (pm20) REVERT: R 54 TYR cc_start: 0.6473 (m-80) cc_final: 0.6170 (m-10) REVERT: S 41 GLN cc_start: 0.6537 (mm-40) cc_final: 0.5863 (tm-30) REVERT: S 51 LYS cc_start: 0.7157 (mtpp) cc_final: 0.6884 (mtpp) REVERT: S 190 TYR cc_start: 0.7975 (m-80) cc_final: 0.7611 (m-80) REVERT: T 322 ILE cc_start: 0.8841 (tp) cc_final: 0.8528 (tt) REVERT: T 398 VAL cc_start: 0.9137 (m) cc_final: 0.8841 (t) REVERT: U 186 GLU cc_start: 0.8119 (tp30) cc_final: 0.7748 (tp30) REVERT: U 213 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7630 (m) REVERT: U 353 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7528 (p0) REVERT: X 82 ASP cc_start: 0.6492 (OUTLIER) cc_final: 0.6226 (p0) REVERT: X 535 LYS cc_start: 0.7782 (mtmm) cc_final: 0.7285 (tttm) REVERT: Y 80 MET cc_start: 0.7826 (mmm) cc_final: 0.7379 (mmm) REVERT: Y 355 PHE cc_start: 0.7921 (m-80) cc_final: 0.7626 (m-10) REVERT: Y 409 ASP cc_start: 0.8622 (t0) cc_final: 0.8073 (t0) REVERT: Y 422 MET cc_start: 0.4102 (OUTLIER) cc_final: 0.3783 (tpt) outliers start: 225 outliers final: 175 residues processed: 831 average time/residue: 0.4707 time to fit residues: 680.7405 Evaluate side-chains 813 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 626 time to evaluate : 4.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 VAL Chi-restraints excluded: chain 0 residue 55 LEU Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 61 MET Chi-restraints excluded: chain 1 residue 107 VAL Chi-restraints excluded: chain 1 residue 123 ILE Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 293 ILE Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 424 VAL Chi-restraints excluded: chain 1 residue 441 PHE Chi-restraints excluded: chain 1 residue 524 THR Chi-restraints excluded: chain 1 residue 532 ILE Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 120 LEU Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 2 residue 223 LYS Chi-restraints excluded: chain 2 residue 278 ASP Chi-restraints excluded: chain 2 residue 390 THR Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 3 residue 119 ASP Chi-restraints excluded: chain 3 residue 126 GLU Chi-restraints excluded: chain 3 residue 161 ILE Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 187 PHE Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 3 residue 239 THR Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 4 residue 142 LEU Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 229 ILE Chi-restraints excluded: chain 4 residue 282 VAL Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 107 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 6 residue 147 SER Chi-restraints excluded: chain 7 residue 38 ASN Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 184 ASN Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 14 THR Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 78 VAL Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 127 PHE Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain S residue 69 LYS Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 315 MET Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 400 SER Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 169 GLN Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 316 THR Chi-restraints excluded: chain U residue 353 ASP Chi-restraints excluded: chain U residue 359 SER Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 405 GLN Chi-restraints excluded: chain U residue 426 SER Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 138 ILE Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 298 LEU Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 394 ILE Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 223 LEU Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 493 LYS Chi-restraints excluded: chain X residue 558 THR Chi-restraints excluded: chain X residue 566 LYS Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 252 ASN Chi-restraints excluded: chain Y residue 263 LEU Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 328 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 422 MET Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 493 LYS Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Z residue 80 MET Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain Z residue 233 ILE Chi-restraints excluded: chain Z residue 297 VAL Chi-restraints excluded: chain Z residue 313 THR Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 407 LEU Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 491 ASP Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 226 optimal weight: 0.9980 chunk 607 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 396 optimal weight: 0.0270 chunk 166 optimal weight: 1.9990 chunk 675 optimal weight: 0.6980 chunk 560 optimal weight: 0.8980 chunk 312 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 354 optimal weight: 6.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 423 ASN 5 107 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 169 GLN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 169 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 386 GLN V 397 ASN ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 54686 Z= 0.164 Angle : 0.570 11.436 74161 Z= 0.284 Chirality : 0.041 0.202 8689 Planarity : 0.004 0.044 9510 Dihedral : 5.672 86.967 7674 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.16 % Favored : 95.74 % Rotamer: Outliers : 3.36 % Allowed : 19.78 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.10), residues: 7038 helix: 0.07 (0.09), residues: 3825 sheet: -0.81 (0.22), residues: 572 loop : -1.04 (0.12), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.011 0.001 HIS V 241 PHE 0.027 0.001 PHE 3 115 TYR 0.025 0.001 TYR 4 211 ARG 0.006 0.000 ARG Z 401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 719 time to evaluate : 4.481 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: 1 261 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8289 (mp) REVERT: 1 441 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7545 (t80) REVERT: 2 74 ASN cc_start: 0.8163 (t0) cc_final: 0.7658 (m-40) REVERT: 2 108 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7274 (tm-30) REVERT: 3 100 GLU cc_start: 0.6079 (mm-30) cc_final: 0.4491 (pt0) REVERT: 5 34 ILE cc_start: 0.8934 (mt) cc_final: 0.8696 (mt) REVERT: 5 63 ASP cc_start: 0.7790 (p0) cc_final: 0.7584 (p0) REVERT: 5 95 MET cc_start: 0.9075 (mmm) cc_final: 0.8546 (mmt) REVERT: 5 104 ASP cc_start: 0.7366 (t0) cc_final: 0.6454 (t0) REVERT: 5 109 GLN cc_start: 0.8304 (mp-120) cc_final: 0.8013 (mt0) REVERT: 5 112 ARG cc_start: 0.7917 (ptt180) cc_final: 0.7263 (ptt-90) REVERT: 6 80 PHE cc_start: 0.7497 (t80) cc_final: 0.6805 (m-10) REVERT: 7 38 ASN cc_start: 0.6822 (OUTLIER) cc_final: 0.6571 (p0) REVERT: 8 69 LYS cc_start: 0.8895 (mttt) cc_final: 0.7478 (tmtt) REVERT: 8 85 THR cc_start: 0.7788 (m) cc_final: 0.7378 (p) REVERT: 9 30 LEU cc_start: 0.7325 (tt) cc_final: 0.6289 (mp) REVERT: 9 35 GLN cc_start: 0.6501 (mm110) cc_final: 0.6286 (mt0) REVERT: 9 69 CYS cc_start: 0.5652 (t) cc_final: 0.5123 (m) REVERT: A 60 LYS cc_start: 0.7114 (mtmt) cc_final: 0.6142 (ptmt) REVERT: B 97 LYS cc_start: 0.6731 (mmtt) cc_final: 0.5912 (mmmt) REVERT: B 122 PHE cc_start: 0.7829 (m-80) cc_final: 0.7539 (m-80) REVERT: C 61 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6359 (mmm) REVERT: C 68 THR cc_start: 0.8084 (p) cc_final: 0.7823 (m) REVERT: D 78 LEU cc_start: 0.8340 (mt) cc_final: 0.7821 (tp) REVERT: E 56 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6513 (pt) REVERT: F 71 LEU cc_start: 0.8219 (tt) cc_final: 0.7150 (mm) REVERT: F 116 PHE cc_start: 0.7442 (m-10) cc_final: 0.7240 (m-80) REVERT: G 113 ILE cc_start: 0.6394 (OUTLIER) cc_final: 0.5990 (tp) REVERT: I 95 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7091 (mm) REVERT: J 122 PHE cc_start: 0.6259 (m-80) cc_final: 0.5963 (m-80) REVERT: M 110 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.8929 (tt) REVERT: M 311 ASN cc_start: 0.8862 (t0) cc_final: 0.8183 (t0) REVERT: M 324 LYS cc_start: 0.7651 (ttpt) cc_final: 0.7066 (mptt) REVERT: P 209 MET cc_start: 0.7726 (mmm) cc_final: 0.7500 (mmp) REVERT: Q 32 LYS cc_start: 0.5952 (tppt) cc_final: 0.5497 (mttp) REVERT: R 54 TYR cc_start: 0.6395 (m-80) cc_final: 0.6130 (m-10) REVERT: S 41 GLN cc_start: 0.6535 (mm-40) cc_final: 0.5927 (tm-30) REVERT: S 51 LYS cc_start: 0.7223 (mtpp) cc_final: 0.6955 (mtpp) REVERT: S 190 TYR cc_start: 0.7887 (m-80) cc_final: 0.7592 (m-80) REVERT: S 197 PHE cc_start: 0.8194 (t80) cc_final: 0.7879 (t80) REVERT: S 238 GLU cc_start: 0.7617 (pm20) cc_final: 0.7049 (pt0) REVERT: T 322 ILE cc_start: 0.8842 (tp) cc_final: 0.8504 (tt) REVERT: T 324 TYR cc_start: 0.8510 (m-80) cc_final: 0.8105 (m-80) REVERT: T 357 LEU cc_start: 0.9151 (tp) cc_final: 0.8921 (tt) REVERT: U 186 GLU cc_start: 0.7993 (tp30) cc_final: 0.7652 (tp30) REVERT: U 213 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7576 (m) REVERT: U 353 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7406 (p0) REVERT: V 553 GLU cc_start: 0.5709 (tp30) cc_final: 0.5485 (tp30) REVERT: X 82 ASP cc_start: 0.6457 (OUTLIER) cc_final: 0.6122 (p0) REVERT: X 416 ILE cc_start: 0.8331 (mm) cc_final: 0.7709 (mt) REVERT: X 435 ARG cc_start: 0.7776 (mtm180) cc_final: 0.7499 (mtm110) REVERT: X 535 LYS cc_start: 0.7772 (mtmm) cc_final: 0.7283 (tttm) REVERT: Y 355 PHE cc_start: 0.7923 (m-80) cc_final: 0.7654 (m-10) REVERT: Y 409 ASP cc_start: 0.8593 (t0) cc_final: 0.8095 (t0) REVERT: Y 422 MET cc_start: 0.3826 (OUTLIER) cc_final: 0.3600 (tpt) outliers start: 189 outliers final: 131 residues processed: 851 average time/residue: 0.4709 time to fit residues: 698.1531 Evaluate side-chains 779 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 636 time to evaluate : 4.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 VAL Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 61 MET Chi-restraints excluded: chain 1 residue 107 VAL Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 293 ILE Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 441 PHE Chi-restraints excluded: chain 1 residue 524 THR Chi-restraints excluded: chain 1 residue 532 ILE Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 120 LEU Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 2 residue 223 LYS Chi-restraints excluded: chain 2 residue 278 ASP Chi-restraints excluded: chain 3 residue 119 ASP Chi-restraints excluded: chain 3 residue 126 GLU Chi-restraints excluded: chain 3 residue 161 ILE Chi-restraints excluded: chain 3 residue 187 PHE Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 150 ASN Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 282 VAL Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 107 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 38 ASN Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 184 ASN Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 14 THR Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 73 TYR Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 78 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 127 PHE Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 384 GLU Chi-restraints excluded: chain T residue 400 SER Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 169 GLN Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 316 THR Chi-restraints excluded: chain U residue 353 ASP Chi-restraints excluded: chain U residue 359 SER Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 298 LEU Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 386 GLN Chi-restraints excluded: chain V residue 397 ASN Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 223 LEU Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 566 LYS Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 328 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 422 MET Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain Z residue 233 ILE Chi-restraints excluded: chain Z residue 247 VAL Chi-restraints excluded: chain Z residue 297 VAL Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 407 LEU Chi-restraints excluded: chain Z residue 491 ASP Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 384 optimal weight: 0.7980 chunk 493 optimal weight: 2.9990 chunk 382 optimal weight: 5.9990 chunk 568 optimal weight: 0.8980 chunk 377 optimal weight: 9.9990 chunk 672 optimal weight: 0.0770 chunk 421 optimal weight: 0.6980 chunk 410 optimal weight: 3.9990 chunk 310 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 423 ASN 4 111 GLN 5 107 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 98 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN R 83 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 72 GLN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 397 ASN ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 398 ASN ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 54686 Z= 0.169 Angle : 0.582 11.979 74161 Z= 0.288 Chirality : 0.042 0.285 8689 Planarity : 0.004 0.046 9510 Dihedral : 5.573 84.426 7674 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.23 % Favored : 95.67 % Rotamer: Outliers : 3.55 % Allowed : 20.46 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.10), residues: 7038 helix: 0.19 (0.09), residues: 3820 sheet: -0.70 (0.22), residues: 592 loop : -1.00 (0.13), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.011 0.001 HIS V 241 PHE 0.027 0.001 PHE B 107 TYR 0.026 0.001 TYR 4 211 ARG 0.006 0.000 ARG Z 401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 686 time to evaluate : 4.656 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: 1 261 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8241 (mp) REVERT: 1 366 MET cc_start: 0.7520 (tpp) cc_final: 0.7225 (tpp) REVERT: 1 441 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7520 (t80) REVERT: 2 74 ASN cc_start: 0.8174 (t0) cc_final: 0.7660 (m-40) REVERT: 2 108 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7261 (tm-30) REVERT: 2 223 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6772 (tppt) REVERT: 3 100 GLU cc_start: 0.6049 (mm-30) cc_final: 0.4499 (pt0) REVERT: 3 106 TRP cc_start: 0.7532 (m-90) cc_final: 0.7259 (m-90) REVERT: 5 34 ILE cc_start: 0.9011 (mt) cc_final: 0.8730 (mt) REVERT: 5 63 ASP cc_start: 0.7794 (p0) cc_final: 0.7578 (p0) REVERT: 5 95 MET cc_start: 0.9095 (mmm) cc_final: 0.8489 (mmt) REVERT: 5 104 ASP cc_start: 0.7363 (t0) cc_final: 0.6392 (t0) REVERT: 5 109 GLN cc_start: 0.8315 (mp-120) cc_final: 0.8030 (mt0) REVERT: 5 112 ARG cc_start: 0.7931 (ptt180) cc_final: 0.7283 (ptt-90) REVERT: 6 80 PHE cc_start: 0.7498 (t80) cc_final: 0.6808 (m-10) REVERT: 7 38 ASN cc_start: 0.6843 (OUTLIER) cc_final: 0.6554 (p0) REVERT: 8 69 LYS cc_start: 0.8925 (mttt) cc_final: 0.7556 (tmtt) REVERT: 8 85 THR cc_start: 0.7949 (m) cc_final: 0.7560 (p) REVERT: 9 30 LEU cc_start: 0.7313 (tt) cc_final: 0.6262 (mp) REVERT: B 122 PHE cc_start: 0.7833 (m-80) cc_final: 0.7562 (m-80) REVERT: C 61 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6395 (mmm) REVERT: C 68 THR cc_start: 0.8070 (p) cc_final: 0.7792 (m) REVERT: D 78 LEU cc_start: 0.8353 (mt) cc_final: 0.7816 (tp) REVERT: D 91 ARG cc_start: 0.7644 (ttt90) cc_final: 0.7290 (mmm160) REVERT: E 56 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6491 (pt) REVERT: F 71 LEU cc_start: 0.8253 (tt) cc_final: 0.7263 (mm) REVERT: F 116 PHE cc_start: 0.7384 (m-10) cc_final: 0.7130 (m-80) REVERT: G 92 ASN cc_start: 0.6929 (OUTLIER) cc_final: 0.6579 (p0) REVERT: J 81 MET cc_start: 0.7914 (tmm) cc_final: 0.7246 (ttt) REVERT: J 122 PHE cc_start: 0.6223 (m-80) cc_final: 0.5911 (m-80) REVERT: M 281 LEU cc_start: 0.8579 (mm) cc_final: 0.8368 (tp) REVERT: M 311 ASN cc_start: 0.8863 (t0) cc_final: 0.8200 (t0) REVERT: M 324 LYS cc_start: 0.7636 (ttpt) cc_final: 0.7037 (mptt) REVERT: Q 32 LYS cc_start: 0.5942 (tppt) cc_final: 0.5523 (mttp) REVERT: R 54 TYR cc_start: 0.6343 (m-80) cc_final: 0.5847 (m-10) REVERT: S 41 GLN cc_start: 0.6560 (mm-40) cc_final: 0.5980 (tm-30) REVERT: S 51 LYS cc_start: 0.7200 (mtpp) cc_final: 0.6961 (mtpp) REVERT: S 190 TYR cc_start: 0.7895 (m-80) cc_final: 0.7602 (m-80) REVERT: S 238 GLU cc_start: 0.7617 (pm20) cc_final: 0.7002 (pt0) REVERT: T 322 ILE cc_start: 0.8845 (tp) cc_final: 0.8498 (tt) REVERT: T 357 LEU cc_start: 0.9148 (tp) cc_final: 0.8943 (tt) REVERT: U 186 GLU cc_start: 0.7992 (tp30) cc_final: 0.7628 (tp30) REVERT: U 213 VAL cc_start: 0.7809 (OUTLIER) cc_final: 0.7490 (m) REVERT: U 353 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7341 (p0) REVERT: X 82 ASP cc_start: 0.6491 (OUTLIER) cc_final: 0.6076 (p0) REVERT: X 416 ILE cc_start: 0.8306 (mm) cc_final: 0.7695 (mt) REVERT: X 435 ARG cc_start: 0.7785 (mtm180) cc_final: 0.7526 (mtm110) REVERT: X 535 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7280 (tttm) REVERT: Y 355 PHE cc_start: 0.7870 (m-80) cc_final: 0.7579 (m-10) REVERT: Y 409 ASP cc_start: 0.8552 (t0) cc_final: 0.8170 (t0) REVERT: Y 422 MET cc_start: 0.3777 (OUTLIER) cc_final: 0.3567 (tpt) outliers start: 200 outliers final: 144 residues processed: 831 average time/residue: 0.4775 time to fit residues: 693.6699 Evaluate side-chains 783 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 628 time to evaluate : 4.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 VAL Chi-restraints excluded: chain 0 residue 55 LEU Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 61 MET Chi-restraints excluded: chain 1 residue 76 GLU Chi-restraints excluded: chain 1 residue 107 VAL Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 213 VAL Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 293 ILE Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 341 GLU Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 441 PHE Chi-restraints excluded: chain 1 residue 524 THR Chi-restraints excluded: chain 1 residue 532 ILE Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 2 residue 223 LYS Chi-restraints excluded: chain 2 residue 278 ASP Chi-restraints excluded: chain 2 residue 390 THR Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 3 residue 119 ASP Chi-restraints excluded: chain 3 residue 126 GLU Chi-restraints excluded: chain 3 residue 187 PHE Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 150 ASN Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 282 VAL Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 107 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 6 residue 147 SER Chi-restraints excluded: chain 7 residue 38 ASN Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 184 ASN Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 14 THR Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 78 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 127 PHE Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 215 LEU Chi-restraints excluded: chain S residue 247 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 224 ILE Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 400 SER Chi-restraints excluded: chain T residue 467 ASP Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 169 GLN Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 316 THR Chi-restraints excluded: chain U residue 353 ASP Chi-restraints excluded: chain U residue 359 SER Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 298 LEU Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 450 LEU Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 223 LEU Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 566 LYS Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 125 ILE Chi-restraints excluded: chain Y residue 252 ASN Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 328 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 422 MET Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain Z residue 233 ILE Chi-restraints excluded: chain Z residue 247 VAL Chi-restraints excluded: chain Z residue 297 VAL Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 407 LEU Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 491 ASP Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 2.9990 chunk 268 optimal weight: 10.0000 chunk 401 optimal weight: 0.9980 chunk 202 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 427 optimal weight: 1.9990 chunk 458 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 528 optimal weight: 0.0270 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 107 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS R 83 GLN S 70 ASN S 250 HIS S 263 ASN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 299 GLN ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 79 HIS ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 408 GLN Z 68 HIS ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 54686 Z= 0.169 Angle : 0.581 12.420 74161 Z= 0.287 Chirality : 0.042 0.223 8689 Planarity : 0.004 0.050 9510 Dihedral : 5.499 82.526 7674 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 3.59 % Allowed : 20.69 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.10), residues: 7038 helix: 0.29 (0.09), residues: 3824 sheet: -0.68 (0.21), residues: 603 loop : -0.96 (0.13), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.011 0.001 HIS V 241 PHE 0.035 0.001 PHE U 203 TYR 0.028 0.001 TYR Y 397 ARG 0.005 0.000 ARG U 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 681 time to evaluate : 4.574 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: 1 261 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8248 (mp) REVERT: 1 366 MET cc_start: 0.7583 (tpp) cc_final: 0.7326 (tpp) REVERT: 1 441 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7506 (t80) REVERT: 2 74 ASN cc_start: 0.8178 (t0) cc_final: 0.7678 (m-40) REVERT: 2 108 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7299 (tm-30) REVERT: 2 223 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6770 (tppt) REVERT: 3 100 GLU cc_start: 0.6007 (mm-30) cc_final: 0.4378 (pt0) REVERT: 3 106 TRP cc_start: 0.7500 (m-90) cc_final: 0.7260 (m-90) REVERT: 4 117 GLU cc_start: 0.7867 (mp0) cc_final: 0.7573 (mp0) REVERT: 5 34 ILE cc_start: 0.8982 (mt) cc_final: 0.8703 (mt) REVERT: 5 63 ASP cc_start: 0.7794 (p0) cc_final: 0.7580 (p0) REVERT: 5 95 MET cc_start: 0.9112 (mmm) cc_final: 0.8551 (mmt) REVERT: 5 104 ASP cc_start: 0.7365 (t0) cc_final: 0.6402 (t0) REVERT: 5 109 GLN cc_start: 0.8285 (mp-120) cc_final: 0.8007 (mt0) REVERT: 5 112 ARG cc_start: 0.7925 (ptt180) cc_final: 0.7295 (ptt-90) REVERT: 6 80 PHE cc_start: 0.7500 (t80) cc_final: 0.6860 (m-10) REVERT: 7 38 ASN cc_start: 0.6841 (OUTLIER) cc_final: 0.6551 (p0) REVERT: 8 69 LYS cc_start: 0.8920 (mttt) cc_final: 0.7550 (tmtt) REVERT: 9 30 LEU cc_start: 0.7345 (tt) cc_final: 0.6205 (mp) REVERT: 9 69 CYS cc_start: 0.5705 (t) cc_final: 0.5066 (m) REVERT: B 122 PHE cc_start: 0.7840 (m-80) cc_final: 0.7561 (m-80) REVERT: C 61 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6440 (mmm) REVERT: C 68 THR cc_start: 0.8073 (p) cc_final: 0.7831 (m) REVERT: C 105 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6429 (tp) REVERT: D 78 LEU cc_start: 0.8382 (mt) cc_final: 0.7811 (tp) REVERT: D 91 ARG cc_start: 0.7625 (ttt90) cc_final: 0.7246 (mmm160) REVERT: E 56 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6384 (pt) REVERT: F 71 LEU cc_start: 0.8248 (tt) cc_final: 0.7259 (mm) REVERT: F 116 PHE cc_start: 0.7318 (m-10) cc_final: 0.7094 (m-80) REVERT: G 92 ASN cc_start: 0.6800 (OUTLIER) cc_final: 0.6412 (p0) REVERT: J 81 MET cc_start: 0.7904 (tmm) cc_final: 0.7435 (ttt) REVERT: J 122 PHE cc_start: 0.6235 (m-80) cc_final: 0.5863 (m-80) REVERT: M 110 LEU cc_start: 0.9427 (tt) cc_final: 0.9221 (tt) REVERT: M 311 ASN cc_start: 0.8870 (t0) cc_final: 0.8231 (t0) REVERT: M 324 LYS cc_start: 0.7624 (ttpt) cc_final: 0.7034 (mptt) REVERT: P 209 MET cc_start: 0.7742 (mmm) cc_final: 0.7444 (mmp) REVERT: Q 14 MET cc_start: 0.5076 (mtt) cc_final: 0.4867 (mtt) REVERT: Q 32 LYS cc_start: 0.5743 (tppt) cc_final: 0.5418 (mttp) REVERT: Q 42 ARG cc_start: 0.5466 (ttp80) cc_final: 0.5120 (ttp80) REVERT: R 54 TYR cc_start: 0.6293 (m-80) cc_final: 0.5785 (m-10) REVERT: S 41 GLN cc_start: 0.6598 (mm-40) cc_final: 0.6116 (tm-30) REVERT: S 51 LYS cc_start: 0.7207 (mtpp) cc_final: 0.6977 (mtpp) REVERT: S 190 TYR cc_start: 0.7921 (m-80) cc_final: 0.7720 (m-80) REVERT: S 238 GLU cc_start: 0.7555 (pm20) cc_final: 0.6937 (pt0) REVERT: T 322 ILE cc_start: 0.8855 (tp) cc_final: 0.8512 (tt) REVERT: T 357 LEU cc_start: 0.9152 (tp) cc_final: 0.8938 (tt) REVERT: U 186 GLU cc_start: 0.8010 (tp30) cc_final: 0.7661 (tp30) REVERT: U 353 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7430 (p0) REVERT: X 82 ASP cc_start: 0.6516 (OUTLIER) cc_final: 0.6100 (p0) REVERT: X 215 GLU cc_start: 0.6496 (tp30) cc_final: 0.5642 (tp30) REVERT: X 416 ILE cc_start: 0.8407 (mm) cc_final: 0.7789 (mt) REVERT: X 435 ARG cc_start: 0.7787 (mtm180) cc_final: 0.7545 (mtm110) REVERT: X 535 LYS cc_start: 0.7724 (mtmm) cc_final: 0.7262 (tttp) REVERT: Y 355 PHE cc_start: 0.7866 (m-80) cc_final: 0.7561 (m-10) REVERT: Y 409 ASP cc_start: 0.8610 (t0) cc_final: 0.8145 (t0) REVERT: Y 414 GLN cc_start: 0.7189 (mm110) cc_final: 0.6844 (mm-40) REVERT: Y 422 MET cc_start: 0.3809 (OUTLIER) cc_final: 0.3597 (tpt) outliers start: 202 outliers final: 154 residues processed: 820 average time/residue: 0.4710 time to fit residues: 676.6201 Evaluate side-chains 810 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 645 time to evaluate : 4.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 VAL Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 61 MET Chi-restraints excluded: chain 1 residue 107 VAL Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 213 VAL Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 293 ILE Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 424 VAL Chi-restraints excluded: chain 1 residue 441 PHE Chi-restraints excluded: chain 1 residue 524 THR Chi-restraints excluded: chain 1 residue 532 ILE Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 120 LEU Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 2 residue 223 LYS Chi-restraints excluded: chain 2 residue 278 ASP Chi-restraints excluded: chain 2 residue 390 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 3 residue 119 ASP Chi-restraints excluded: chain 3 residue 126 GLU Chi-restraints excluded: chain 3 residue 161 ILE Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 150 ASN Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 282 VAL Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 107 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 6 residue 147 SER Chi-restraints excluded: chain 7 residue 38 ASN Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 14 THR Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 78 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 102 TYR Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 127 PHE Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain S residue 45 GLN Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 215 LEU Chi-restraints excluded: chain S residue 247 THR Chi-restraints excluded: chain S residue 271 MET Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 244 ASN Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 400 SER Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 169 GLN Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 316 THR Chi-restraints excluded: chain U residue 353 ASP Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 298 LEU Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 439 MET Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 223 LEU Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 566 LYS Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 125 ILE Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 252 ASN Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 328 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 422 MET Chi-restraints excluded: chain Z residue 80 MET Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 192 LEU Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain Z residue 233 ILE Chi-restraints excluded: chain Z residue 247 VAL Chi-restraints excluded: chain Z residue 297 VAL Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 373 ILE Chi-restraints excluded: chain Z residue 407 LEU Chi-restraints excluded: chain Z residue 491 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 10.0000 chunk 644 optimal weight: 7.9990 chunk 588 optimal weight: 10.0000 chunk 626 optimal weight: 2.9990 chunk 377 optimal weight: 0.9980 chunk 273 optimal weight: 5.9990 chunk 492 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 566 optimal weight: 4.9990 chunk 592 optimal weight: 5.9990 chunk 624 optimal weight: 0.2980 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 124 ASN 5 107 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 267 HIS U 319 HIS ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 386 GLN V 397 ASN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 398 ASN Z 68 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 54686 Z= 0.307 Angle : 0.660 11.066 74161 Z= 0.330 Chirality : 0.045 0.333 8689 Planarity : 0.004 0.056 9510 Dihedral : 5.790 86.430 7674 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.10 % Favored : 94.76 % Rotamer: Outliers : 3.71 % Allowed : 20.96 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.10), residues: 7038 helix: 0.11 (0.09), residues: 3823 sheet: -0.81 (0.21), residues: 616 loop : -1.04 (0.13), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 3 106 HIS 0.009 0.001 HIS V 241 PHE 0.023 0.002 PHE U 508 TYR 0.034 0.002 TYR G 102 ARG 0.006 0.001 ARG M 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 639 time to evaluate : 4.654 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: 1 441 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7594 (t80) REVERT: 2 108 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7234 (tm-30) REVERT: 3 100 GLU cc_start: 0.6240 (mm-30) cc_final: 0.4438 (pt0) REVERT: 4 142 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7954 (tp) REVERT: 4 204 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: 5 63 ASP cc_start: 0.7934 (p0) cc_final: 0.7670 (p0) REVERT: 5 95 MET cc_start: 0.9147 (mmm) cc_final: 0.8702 (mmt) REVERT: 5 104 ASP cc_start: 0.7660 (t0) cc_final: 0.6587 (t0) REVERT: 5 109 GLN cc_start: 0.8309 (mp-120) cc_final: 0.8059 (mt0) REVERT: 5 112 ARG cc_start: 0.7969 (ptt180) cc_final: 0.7325 (ptt-90) REVERT: 6 80 PHE cc_start: 0.7378 (t80) cc_final: 0.6791 (m-10) REVERT: 7 38 ASN cc_start: 0.6760 (OUTLIER) cc_final: 0.6472 (p0) REVERT: 8 69 LYS cc_start: 0.8959 (mttt) cc_final: 0.7519 (tmtt) REVERT: 9 30 LEU cc_start: 0.7505 (tt) cc_final: 0.6403 (mp) REVERT: 9 69 CYS cc_start: 0.5554 (t) cc_final: 0.4859 (m) REVERT: A 60 LYS cc_start: 0.7270 (mtmt) cc_final: 0.6493 (ttpp) REVERT: B 122 PHE cc_start: 0.7969 (m-80) cc_final: 0.7609 (m-80) REVERT: C 61 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6424 (mmm) REVERT: C 68 THR cc_start: 0.8158 (p) cc_final: 0.7909 (m) REVERT: D 91 ARG cc_start: 0.7369 (ttt90) cc_final: 0.7099 (mmm160) REVERT: E 56 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6380 (pt) REVERT: F 71 LEU cc_start: 0.8128 (tt) cc_final: 0.7110 (mm) REVERT: F 116 PHE cc_start: 0.7351 (m-10) cc_final: 0.7109 (m-80) REVERT: G 92 ASN cc_start: 0.6919 (OUTLIER) cc_final: 0.6533 (p0) REVERT: J 81 MET cc_start: 0.7952 (tmm) cc_final: 0.7688 (ttt) REVERT: J 122 PHE cc_start: 0.6393 (m-80) cc_final: 0.5971 (m-80) REVERT: M 324 LYS cc_start: 0.7674 (ttpt) cc_final: 0.7123 (mptt) REVERT: Q 14 MET cc_start: 0.5332 (mtt) cc_final: 0.5058 (mtt) REVERT: Q 42 ARG cc_start: 0.5807 (ttp80) cc_final: 0.5335 (ttp80) REVERT: R 54 TYR cc_start: 0.6483 (m-80) cc_final: 0.6253 (m-10) REVERT: S 41 GLN cc_start: 0.6716 (mm-40) cc_final: 0.6340 (tm-30) REVERT: S 51 LYS cc_start: 0.7221 (mtpp) cc_final: 0.6948 (mtpp) REVERT: S 190 TYR cc_start: 0.8128 (m-80) cc_final: 0.7789 (m-80) REVERT: T 322 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8608 (tt) REVERT: U 186 GLU cc_start: 0.8048 (tp30) cc_final: 0.7708 (tp30) REVERT: U 353 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7589 (p0) REVERT: U 439 MET cc_start: 0.6799 (tpp) cc_final: 0.6596 (tpp) REVERT: X 82 ASP cc_start: 0.6521 (OUTLIER) cc_final: 0.6135 (p0) REVERT: X 215 GLU cc_start: 0.6602 (tp30) cc_final: 0.5895 (tp30) REVERT: X 321 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8836 (tp) REVERT: X 435 ARG cc_start: 0.7838 (mtm180) cc_final: 0.7586 (mtm110) REVERT: Y 355 PHE cc_start: 0.7985 (m-80) cc_final: 0.7606 (m-10) REVERT: Y 409 ASP cc_start: 0.8671 (t0) cc_final: 0.8134 (t0) REVERT: Y 414 GLN cc_start: 0.7344 (mm110) cc_final: 0.6964 (mm-40) REVERT: Y 422 MET cc_start: 0.3964 (OUTLIER) cc_final: 0.3361 (tpp) REVERT: Z 215 GLU cc_start: 0.7830 (tp30) cc_final: 0.7230 (tp30) REVERT: Z 345 ASP cc_start: 0.7056 (m-30) cc_final: 0.6805 (m-30) outliers start: 209 outliers final: 179 residues processed: 786 average time/residue: 0.4717 time to fit residues: 651.2119 Evaluate side-chains 800 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 609 time to evaluate : 4.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 VAL Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 58 GLU Chi-restraints excluded: chain 1 residue 61 MET Chi-restraints excluded: chain 1 residue 107 VAL Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 213 VAL Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 293 ILE Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 424 VAL Chi-restraints excluded: chain 1 residue 441 PHE Chi-restraints excluded: chain 1 residue 524 THR Chi-restraints excluded: chain 1 residue 532 ILE Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 120 LEU Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 2 residue 223 LYS Chi-restraints excluded: chain 2 residue 278 ASP Chi-restraints excluded: chain 2 residue 390 THR Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 3 residue 119 ASP Chi-restraints excluded: chain 3 residue 126 GLU Chi-restraints excluded: chain 3 residue 161 ILE Chi-restraints excluded: chain 3 residue 187 PHE Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 4 residue 116 SER Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 142 LEU Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 150 ASN Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 204 PHE Chi-restraints excluded: chain 4 residue 229 ILE Chi-restraints excluded: chain 4 residue 282 VAL Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 107 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 38 ASN Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 184 ASN Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 78 VAL Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 127 PHE Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain S residue 45 GLN Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 215 LEU Chi-restraints excluded: chain S residue 247 THR Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 271 MET Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 244 ASN Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 169 GLN Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 316 THR Chi-restraints excluded: chain U residue 353 ASP Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 535 ILE Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 258 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 298 LEU Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 386 GLN Chi-restraints excluded: chain V residue 397 ASN Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 439 MET Chi-restraints excluded: chain V residue 450 LEU Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 223 LEU Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 321 LEU Chi-restraints excluded: chain X residue 493 LYS Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 566 LYS Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 125 ILE Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 252 ASN Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 328 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 422 MET Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 68 HIS Chi-restraints excluded: chain Z residue 80 MET Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 192 LEU Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain Z residue 233 ILE Chi-restraints excluded: chain Z residue 247 VAL Chi-restraints excluded: chain Z residue 297 VAL Chi-restraints excluded: chain Z residue 313 THR Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 407 LEU Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 491 ASP Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 0.9990 chunk 662 optimal weight: 10.0000 chunk 404 optimal weight: 9.9990 chunk 314 optimal weight: 5.9990 chunk 460 optimal weight: 8.9990 chunk 695 optimal weight: 10.0000 chunk 640 optimal weight: 0.0020 chunk 553 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 427 optimal weight: 20.0000 chunk 339 optimal weight: 9.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 124 ASN ** 4 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 107 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN I 98 GLN M 243 ASN ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 397 ASN ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 54686 Z= 0.245 Angle : 0.628 13.228 74161 Z= 0.313 Chirality : 0.043 0.294 8689 Planarity : 0.004 0.058 9510 Dihedral : 5.738 86.991 7674 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.21 % Rotamer: Outliers : 3.50 % Allowed : 21.54 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.10), residues: 7038 helix: 0.20 (0.09), residues: 3820 sheet: -0.83 (0.21), residues: 618 loop : -0.98 (0.13), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 9 73 HIS 0.010 0.001 HIS V 241 PHE 0.032 0.001 PHE G 122 TYR 0.026 0.001 TYR G 102 ARG 0.006 0.000 ARG V 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 625 time to evaluate : 4.510 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: 1 441 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7623 (t80) REVERT: 2 74 ASN cc_start: 0.8275 (t0) cc_final: 0.7623 (m-40) REVERT: 2 108 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7396 (tm-30) REVERT: 3 100 GLU cc_start: 0.6173 (mm-30) cc_final: 0.4416 (pt0) REVERT: 4 204 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: 5 63 ASP cc_start: 0.7951 (p0) cc_final: 0.7651 (p0) REVERT: 5 95 MET cc_start: 0.9132 (mmm) cc_final: 0.8646 (mmt) REVERT: 5 104 ASP cc_start: 0.7568 (t0) cc_final: 0.6457 (t0) REVERT: 5 112 ARG cc_start: 0.7954 (ptt180) cc_final: 0.7302 (ptt-90) REVERT: 6 80 PHE cc_start: 0.7425 (t80) cc_final: 0.6811 (m-10) REVERT: 7 38 ASN cc_start: 0.6667 (OUTLIER) cc_final: 0.6375 (p0) REVERT: 8 69 LYS cc_start: 0.8934 (mttt) cc_final: 0.7526 (tmtt) REVERT: 9 30 LEU cc_start: 0.7520 (tt) cc_final: 0.6430 (mp) REVERT: 9 69 CYS cc_start: 0.5779 (t) cc_final: 0.4981 (m) REVERT: A 60 LYS cc_start: 0.7082 (mtmt) cc_final: 0.6315 (ttpp) REVERT: B 61 MET cc_start: 0.6920 (mmp) cc_final: 0.6705 (mmt) REVERT: B 122 PHE cc_start: 0.7922 (m-80) cc_final: 0.7596 (m-80) REVERT: C 61 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6674 (mmm) REVERT: C 68 THR cc_start: 0.8280 (p) cc_final: 0.8046 (m) REVERT: D 91 ARG cc_start: 0.7319 (ttt90) cc_final: 0.7072 (mmm160) REVERT: E 56 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6380 (pt) REVERT: F 71 LEU cc_start: 0.8141 (tt) cc_final: 0.7127 (mm) REVERT: F 116 PHE cc_start: 0.7340 (m-10) cc_final: 0.7102 (m-80) REVERT: G 92 ASN cc_start: 0.6741 (OUTLIER) cc_final: 0.6355 (p0) REVERT: J 61 MET cc_start: 0.6174 (mmm) cc_final: 0.5759 (mmm) REVERT: J 122 PHE cc_start: 0.6350 (m-80) cc_final: 0.5945 (m-80) REVERT: M 110 LEU cc_start: 0.9515 (tt) cc_final: 0.9292 (tt) REVERT: M 324 LYS cc_start: 0.7687 (ttpt) cc_final: 0.7137 (mptt) REVERT: Q 14 MET cc_start: 0.5249 (mtt) cc_final: 0.5006 (mtt) REVERT: Q 42 ARG cc_start: 0.5668 (ttp80) cc_final: 0.5233 (ttp80) REVERT: R 54 TYR cc_start: 0.6473 (m-80) cc_final: 0.6242 (m-10) REVERT: S 41 GLN cc_start: 0.6730 (mm-40) cc_final: 0.6381 (tm-30) REVERT: S 51 LYS cc_start: 0.7199 (mtpp) cc_final: 0.6924 (mtpp) REVERT: T 322 ILE cc_start: 0.8876 (tp) cc_final: 0.8570 (tt) REVERT: U 186 GLU cc_start: 0.8139 (tp30) cc_final: 0.7865 (tp30) REVERT: U 353 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7487 (p0) REVERT: U 439 MET cc_start: 0.6792 (tpp) cc_final: 0.6591 (tpp) REVERT: X 82 ASP cc_start: 0.6498 (OUTLIER) cc_final: 0.6097 (p0) REVERT: X 215 GLU cc_start: 0.6493 (tp30) cc_final: 0.5998 (tp30) REVERT: X 321 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8852 (tp) REVERT: X 435 ARG cc_start: 0.7853 (mtm180) cc_final: 0.7599 (mtm110) REVERT: Y 355 PHE cc_start: 0.7981 (m-80) cc_final: 0.7593 (m-10) REVERT: Y 409 ASP cc_start: 0.8657 (t0) cc_final: 0.8094 (t0) REVERT: Y 414 GLN cc_start: 0.7254 (mm110) cc_final: 0.6888 (mm-40) REVERT: Y 422 MET cc_start: 0.3892 (OUTLIER) cc_final: 0.3331 (tpp) REVERT: Z 215 GLU cc_start: 0.7799 (tp30) cc_final: 0.7203 (tp30) REVERT: Z 345 ASP cc_start: 0.7045 (m-30) cc_final: 0.6777 (m-30) REVERT: Z 486 PHE cc_start: 0.5967 (m-80) cc_final: 0.5671 (m-10) outliers start: 197 outliers final: 173 residues processed: 766 average time/residue: 0.4802 time to fit residues: 642.3005 Evaluate side-chains 793 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 610 time to evaluate : 4.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 VAL Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 58 GLU Chi-restraints excluded: chain 1 residue 61 MET Chi-restraints excluded: chain 1 residue 107 VAL Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 213 VAL Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 293 ILE Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 424 VAL Chi-restraints excluded: chain 1 residue 441 PHE Chi-restraints excluded: chain 1 residue 524 THR Chi-restraints excluded: chain 1 residue 532 ILE Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 120 LEU Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 2 residue 223 LYS Chi-restraints excluded: chain 2 residue 278 ASP Chi-restraints excluded: chain 2 residue 390 THR Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 3 residue 119 ASP Chi-restraints excluded: chain 3 residue 126 GLU Chi-restraints excluded: chain 3 residue 161 ILE Chi-restraints excluded: chain 3 residue 187 PHE Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 4 residue 116 SER Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 150 ASN Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 204 PHE Chi-restraints excluded: chain 4 residue 229 ILE Chi-restraints excluded: chain 4 residue 282 VAL Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 107 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 38 ASN Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 184 ASN Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 78 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 243 ASN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 127 PHE Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain S residue 45 GLN Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 215 LEU Chi-restraints excluded: chain S residue 247 THR Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 271 MET Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 244 ASN Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 467 ASP Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 169 GLN Chi-restraints excluded: chain U residue 316 THR Chi-restraints excluded: chain U residue 353 ASP Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 484 LEU Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 258 VAL Chi-restraints excluded: chain V residue 298 LEU Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 394 ILE Chi-restraints excluded: chain V residue 397 ASN Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 439 MET Chi-restraints excluded: chain V residue 450 LEU Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 223 LEU Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 321 LEU Chi-restraints excluded: chain X residue 493 LYS Chi-restraints excluded: chain X residue 566 LYS Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 125 ILE Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 252 ASN Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 328 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 422 MET Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 80 MET Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 192 LEU Chi-restraints excluded: chain Z residue 222 ASP Chi-restraints excluded: chain Z residue 233 ILE Chi-restraints excluded: chain Z residue 247 VAL Chi-restraints excluded: chain Z residue 297 VAL Chi-restraints excluded: chain Z residue 313 THR Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 407 LEU Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 491 ASP Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 0.9980 chunk 589 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 510 optimal weight: 0.4980 chunk 81 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 554 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 569 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 562 ASN 4 124 ASN 5 107 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 471 GLN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 248 GLN V 397 ASN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 398 ASN Z 68 HIS ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.122270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.103120 restraints weight = 122234.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.102869 restraints weight = 100083.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.103663 restraints weight = 87109.076| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 54686 Z= 0.169 Angle : 0.599 13.004 74161 Z= 0.296 Chirality : 0.042 0.260 8689 Planarity : 0.004 0.055 9510 Dihedral : 5.544 83.571 7674 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 3.09 % Allowed : 21.91 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.10), residues: 7038 helix: 0.36 (0.09), residues: 3828 sheet: -0.62 (0.22), residues: 589 loop : -0.89 (0.13), residues: 2621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 9 73 HIS 0.011 0.001 HIS V 241 PHE 0.035 0.001 PHE 7 185 TYR 0.037 0.001 TYR S 190 ARG 0.007 0.000 ARG M 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11716.91 seconds wall clock time: 207 minutes 27.12 seconds (12447.12 seconds total)