Starting phenix.real_space_refine on Tue Feb 13 06:28:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rep_4853/02_2024/6rep_4853_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rep_4853/02_2024/6rep_4853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rep_4853/02_2024/6rep_4853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rep_4853/02_2024/6rep_4853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rep_4853/02_2024/6rep_4853_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rep_4853/02_2024/6rep_4853_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34301 2.51 5 N 9113 2.21 5 O 10200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 ARG 150": "NH1" <-> "NH2" Residue "1 ASP 172": "OD1" <-> "OD2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 215": "OE1" <-> "OE2" Residue "1 GLU 229": "OE1" <-> "OE2" Residue "1 GLU 258": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 341": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 GLU 352": "OE1" <-> "OE2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 GLU 385": "OE1" <-> "OE2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 ASP 425": "OD1" <-> "OD2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 442": "OD1" <-> "OD2" Residue "1 GLU 457": "OE1" <-> "OE2" Residue "1 ASP 486": "OD1" <-> "OD2" Residue "1 GLU 496": "OE1" <-> "OE2" Residue "1 GLU 577": "OE1" <-> "OE2" Residue "1 ASP 578": "OD1" <-> "OD2" Residue "1 ASP 601": "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 86": "OE1" <-> "OE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 154": "OD1" <-> "OD2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 230": "OD1" <-> "OD2" Residue "2 GLU 246": "OE1" <-> "OE2" Residue "2 TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 346": "NH1" <-> "NH2" Residue "2 ASP 367": "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 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 162": "OE1" <-> "OE2" Residue "3 PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 175": "OE1" <-> "OE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 213": "NH1" <-> "NH2" Residue "3 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 233": "NH1" <-> "NH2" Residue "3 ARG 242": "NH1" <-> "NH2" Residue "3 ARG 257": "NH1" <-> "NH2" Residue "3 ASP 259": "OD1" <-> "OD2" Residue "3 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 320": "OE1" <-> "OE2" Residue "4 ASP 19": "OD1" <-> "OD2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 40": "OE1" <-> "OE2" Residue "4 TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 64": "OE1" <-> "OE2" Residue "4 ARG 84": "NH1" <-> "NH2" Residue "4 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 117": "OE1" <-> "OE2" Residue "4 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 176": "NH1" <-> "NH2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 193": "OE1" <-> "OE2" Residue "4 PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 271": "OD1" <-> "OD2" Residue "4 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 6": "OE1" <-> "OE2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 GLU 37": "OE1" <-> "OE2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 53": "OE1" <-> "OE2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "5 PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 47": "OE1" <-> "OE2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 109": "OD1" <-> "OD2" Residue "7 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 117": "OD1" <-> "OD2" Residue "7 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 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 62": "OD1" <-> "OD2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "8 TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 17": "OD1" <-> "OD2" Residue "9 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 40": "NH1" <-> "NH2" Residue "9 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 74": "OE1" <-> "OE2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "J GLU 111": "OE1" <-> "OE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M ASP 128": "OD1" <-> "OD2" Residue "M ARG 145": "NH1" <-> "NH2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 239": "NH1" <-> "NH2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 72": "OD1" <-> "OD2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 116": "OE1" <-> "OE2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 166": "OE1" <-> "OE2" Residue "P PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 191": "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 ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 64": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 95": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 186": "OE1" <-> "OE2" Residue "R GLU 196": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 83": "OD1" <-> "OD2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 214": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S GLU 283": "OE1" <-> "OE2" Residue "S ASP 291": "OD1" <-> "OD2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 303": "OE1" <-> "OE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ASP 46": "OD1" <-> "OD2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T GLU 74": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ARG 96": "NH1" <-> "NH2" Residue "T ASP 112": "OD1" <-> "OD2" Residue "T TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 247": "OE1" <-> "OE2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 411": "OE1" <-> "OE2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "NH1" <-> "NH2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T GLU 455": "OE1" <-> "OE2" Residue "T PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 495": "OE1" <-> "OE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 510": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 92": "OD1" <-> "OD2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 125": "OD1" <-> "OD2" Residue "U ASP 135": "OD1" <-> "OD2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ASP 237": "OD1" <-> "OD2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 311": "OE1" <-> "OE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 409": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 465": "OD1" <-> "OD2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U ASP 516": "OD1" <-> "OD2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 547": "OD1" <-> "OD2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 403": "OD1" <-> "OD2" Residue "V PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 449": "OE1" <-> "OE2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V GLU 455": "OE1" <-> "OE2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ASP 82": "OD1" <-> "OD2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ASP 94": "OD1" <-> "OD2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X GLU 131": "OE1" <-> "OE2" Residue "X ASP 136": "OD1" <-> "OD2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 168": "OD1" <-> "OD2" Residue "X TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X GLU 270": "OE1" <-> "OE2" Residue "X ASP 279": "OD1" <-> "OD2" Residue "X PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 317": "OD1" <-> "OD2" Residue "X ASP 345": "OD1" <-> "OD2" Residue "X ASP 348": "OD1" <-> "OD2" Residue "X ARG 366": "NH1" <-> "NH2" Residue "X GLU 370": "OE1" <-> "OE2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X GLU 427": "OE1" <-> "OE2" Residue "X PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 451": "OE1" <-> "OE2" Residue "X PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 465": "OD1" <-> "OD2" Residue "X PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 480": "OD1" <-> "OD2" Residue "X PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 491": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 520": "OE1" <-> "OE2" Residue "X ASP 523": "OD1" <-> "OD2" Residue "X GLU 541": "OE1" <-> "OE2" Residue "X ASP 542": "OD1" <-> "OD2" Residue "X GLU 547": "OE1" <-> "OE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y GLU 55": "OE1" <-> "OE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ASP 94": "OD1" <-> "OD2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y GLU 149": "OE1" <-> "OE2" Residue "Y PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 215": "OE1" <-> "OE2" Residue "Y ARG 216": "NH1" <-> "NH2" Residue "Y GLU 226": "OE1" <-> "OE2" Residue "Y GLU 229": "OE1" <-> "OE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y ASP 285": "OD1" <-> "OD2" Residue "Y ARG 289": "NH1" <-> "NH2" Residue "Y ASP 344": "OD1" <-> "OD2" Residue "Y ASP 345": "OD1" <-> "OD2" Residue "Y ASP 348": "OD1" <-> "OD2" Residue "Y PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 370": "OE1" <-> "OE2" Residue "Y ASP 378": "OD1" <-> "OD2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ARG 401": "NH1" <-> "NH2" Residue "Y TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 435": "NH1" <-> "NH2" Residue "Y ARG 437": "NH1" <-> "NH2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 465": "OD1" <-> "OD2" Residue "Y ASP 479": "OD1" <-> "OD2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 552": "OE1" <-> "OE2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z ASP 136": "OD1" <-> "OD2" Residue "Z ASP 139": "OD1" <-> "OD2" Residue "Z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 218": "NH1" <-> "NH2" Residue "Z GLU 219": "OE1" <-> "OE2" Residue "Z ARG 225": "NH1" <-> "NH2" Residue "Z ARG 239": "NH1" <-> "NH2" Residue "Z TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 296": "OE1" <-> "OE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 378": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z ASP 415": "OD1" <-> "OD2" Residue "Z ASP 423": "OD1" <-> "OD2" Residue "Z PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z GLU 519": "OE1" <-> "OE2" Residue "Z GLU 536": "OE1" <-> "OE2" Residue "Z GLU 540": "OE1" <-> "OE2" Residue "Z GLU 541": "OE1" <-> "OE2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 552": "OE1" <-> "OE2" Residue "Z GLU 563": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 53782 Number of models: 1 Model: "" Number of chains: 43 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 20.62, per 1000 atoms: 0.38 Number of scatterers: 53782 At special positions: 0 Unit cell: (214.812, 133.731, 263.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 149 16.00 P 13 15.00 Mg 5 11.99 O 10200 8.00 N 9113 7.00 C 34301 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.58 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 300 helices and 29 sheets defined 51.6% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.84 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 removed outlier: 3.614A pdb=" N LYS 1 68 " --> pdb=" O LEU 1 64 " (cutoff:3.500A) Processing helix chain '1' and resid 97 through 99 No H-bonds generated for 'chain '1' and resid 97 through 99' Processing helix chain '1' and resid 107 through 141 removed outlier: 3.780A pdb=" N ALA 1 121 " --> pdb=" O THR 1 117 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA 1 122 " --> pdb=" O ARG 1 118 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE 1 129 " --> pdb=" O SER 1 125 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR 1 135 " --> pdb=" O ALA 1 131 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA 1 139 " --> pdb=" O THR 1 135 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) Processing helix chain '1' and resid 164 through 175 removed outlier: 3.868A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 204 removed outlier: 3.773A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP 1 199 " --> pdb=" O LYS 1 195 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE 1 200 " --> pdb=" O ALA 1 196 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL 1 204 " --> pdb=" O PHE 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 210 through 223 removed outlier: 3.582A pdb=" N LEU 1 216 " --> pdb=" O GLU 1 212 " (cutoff:3.500A) Processing helix chain '1' and resid 244 through 270 removed outlier: 3.687A pdb=" N ARG 1 259 " --> pdb=" O GLU 1 255 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS 1 266 " --> pdb=" O LYS 1 262 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL 1 270 " --> pdb=" O LYS 1 266 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 276 removed outlier: 3.549A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 283 through 285 No H-bonds generated for 'chain '1' and resid 283 through 285' Processing helix chain '1' and resid 290 through 292 No H-bonds generated for 'chain '1' and resid 290 through 292' Processing helix chain '1' and resid 298 through 306 removed outlier: 3.654A pdb=" N ALA 1 303 " --> pdb=" O GLU 1 299 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN 1 306 " --> pdb=" O SER 1 302 " (cutoff:3.500A) Processing helix chain '1' and resid 311 through 316 Processing helix chain '1' and resid 319 through 321 No H-bonds generated for 'chain '1' and resid 319 through 321' 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 removed outlier: 3.849A pdb=" N ARG 1 381 " --> pdb=" O SER 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 393 through 417 removed outlier: 3.821A pdb=" N GLU 1 415 " --> pdb=" O ALA 1 411 " (cutoff:3.500A) Processing helix chain '1' and resid 426 through 431 Processing helix chain '1' and resid 436 through 444 removed outlier: 3.713A pdb=" N PHE 1 441 " --> pdb=" O VAL 1 437 " (cutoff:3.500A) Processing helix chain '1' and resid 447 through 458 Processing helix chain '1' and resid 464 through 477 removed outlier: 3.659A pdb=" N THR 1 471 " --> pdb=" O ALA 1 467 " (cutoff:3.500A) 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: 3.592A pdb=" N GLU 1 495 " --> pdb=" O PRO 1 491 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU 1 496 " --> pdb=" O GLN 1 492 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER 1 503 " --> pdb=" O GLU 1 499 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP 1 508 " --> pdb=" O ASP 1 504 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU 1 512 " --> pdb=" O ASP 1 508 " (cutoff:3.500A) Processing helix chain '1' and resid 519 through 535 removed outlier: 3.643A pdb=" N THR 1 526 " --> pdb=" O LEU 1 522 " (cutoff:3.500A) Processing helix chain '1' and resid 542 through 548 Processing helix chain '1' and resid 550 through 561 Processing helix chain '1' and resid 567 through 573 Processing helix chain '1' and resid 577 through 587 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 593 through 605 removed outlier: 3.530A pdb=" N ALA 1 603 " --> pdb=" O ARG 1 599 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 26 through 38 Processing helix chain '2' and resid 45 through 57 removed outlier: 3.642A pdb=" N GLY 2 56 " --> pdb=" O LEU 2 52 " (cutoff:3.500A) Processing helix chain '2' and resid 63 through 75 removed outlier: 3.533A pdb=" N THR 2 67 " --> pdb=" O ALA 2 63 " (cutoff:3.500A) Processing helix chain '2' and resid 81 through 93 removed outlier: 3.819A pdb=" N ALA 2 88 " --> pdb=" O VAL 2 84 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY 2 89 " --> pdb=" O ALA 2 85 " (cutoff:3.500A) Proline residue: 2 90 - end of helix Processing helix chain '2' and resid 100 through 112 removed outlier: 3.504A pdb=" N SER 2 104 " --> pdb=" O PRO 2 100 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE 2 105 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 118 through 128 removed outlier: 3.596A pdb=" N ALA 2 126 " --> pdb=" O ASN 2 122 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL 2 128 " --> pdb=" O ALA 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 137 through 149 removed outlier: 3.697A pdb=" N ARG 2 142 " --> pdb=" O ALA 2 138 " (cutoff:3.500A) Processing helix chain '2' and resid 155 through 167 removed outlier: 3.746A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) Processing helix chain '2' and resid 172 through 185 removed outlier: 3.526A pdb=" N LYS 2 184 " --> pdb=" O TYR 2 180 " (cutoff:3.500A) Processing helix chain '2' and resid 190 through 199 removed outlier: 3.526A pdb=" N ASP 2 194 " --> pdb=" O LYS 2 190 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER 2 199 " --> pdb=" O ALA 2 195 " (cutoff:3.500A) Processing helix chain '2' and resid 208 through 219 Processing helix chain '2' and resid 228 through 231 No H-bonds generated for 'chain '2' and resid 228 through 231' Processing helix chain '2' and resid 241 through 253 removed outlier: 3.648A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 259 through 275 removed outlier: 3.671A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.785A 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 282 through 294 removed outlier: 3.687A pdb=" N GLN 2 287 " --> pdb=" O SER 2 283 " (cutoff:3.500A) Processing helix chain '2' and resid 301 through 320 removed outlier: 3.539A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP 2 316 " --> pdb=" O GLY 2 312 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA 2 318 " --> pdb=" O ALA 2 314 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 340 Processing helix chain '2' and resid 346 through 353 removed outlier: 3.591A pdb=" N ALA 2 352 " --> pdb=" O GLU 2 348 " (cutoff:3.500A) Processing helix chain '2' and resid 397 through 409 removed outlier: 3.589A pdb=" N ARG 2 406 " --> pdb=" O TYR 2 402 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 421 No H-bonds generated for 'chain '2' and resid 418 through 421' Processing helix chain '2' and resid 427 through 441 removed outlier: 3.594A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 86 Processing helix chain '3' and resid 92 through 95 No H-bonds generated for 'chain '3' and resid 92 through 95' Processing helix chain '3' and resid 103 through 112 removed outlier: 3.576A pdb=" N TYR 3 108 " --> pdb=" O PRO 3 104 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU 3 110 " --> pdb=" O TRP 3 106 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 124 removed outlier: 3.783A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 134 No H-bonds generated for 'chain '3' and resid 132 through 134' Processing helix chain '3' and resid 137 through 149 removed outlier: 3.629A pdb=" N VAL 3 145 " --> pdb=" O THR 3 141 " (cutoff:3.500A) Processing helix chain '3' and resid 155 through 167 removed outlier: 4.151A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 169 through 171 No H-bonds generated for 'chain '3' and resid 169 through 171' Processing helix chain '3' and resid 174 through 186 removed outlier: 3.860A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 192 through 203 Processing helix chain '3' and resid 216 through 229 removed outlier: 4.060A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 240 Processing helix chain '3' and resid 246 through 250 Processing helix chain '3' and resid 254 through 270 Processing helix chain '3' and resid 276 through 278 No H-bonds generated for 'chain '3' and resid 276 through 278' Processing helix chain '3' and resid 289 through 291 No H-bonds generated for 'chain '3' and resid 289 through 291' Processing helix chain '3' and resid 294 through 311 removed outlier: 3.848A pdb=" N LYS 3 298 " --> pdb=" O ALA 3 294 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN 3 309 " --> pdb=" O VAL 3 305 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA 3 310 " --> pdb=" O ALA 3 306 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 14 Processing helix chain '4' and resid 20 through 34 removed outlier: 3.522A pdb=" N TYR 4 34 " --> pdb=" O LEU 4 30 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 69 removed outlier: 4.064A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.712A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN 4 69 " --> pdb=" O PRO 4 65 " (cutoff:3.500A) Processing helix chain '4' and resid 80 through 95 Processing helix chain '4' and resid 101 through 112 Processing helix chain '4' and resid 119 through 123 Processing helix chain '4' and resid 132 through 137 removed outlier: 3.530A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) Processing helix chain '4' and resid 139 through 149 removed outlier: 4.641A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 176 removed outlier: 3.687A pdb=" N PHE 4 165 " --> pdb=" O GLY 4 161 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.932A 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: 3.597A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP 4 206 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA 4 213 " --> pdb=" O SER 4 209 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA 4 217 " --> pdb=" O ALA 4 213 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 258 removed outlier: 3.610A 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 28 Processing helix chain '5' and resid 31 through 58 removed outlier: 3.716A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN 5 52 " --> pdb=" O ALA 5 48 " (cutoff:3.500A) Processing helix chain '5' and resid 73 through 80 Processing helix chain '5' and resid 89 through 105 removed outlier: 3.718A pdb=" N SER 5 97 " --> pdb=" O GLU 5 93 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL 5 102 " --> pdb=" O ALA 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 118 removed outlier: 4.334A pdb=" N VAL 5 118 " --> pdb=" O ILE 5 115 " (cutoff:3.500A) Processing helix chain '6' and resid 31 through 40 Processing helix chain '6' and resid 48 through 57 removed outlier: 3.867A pdb=" N LEU 6 51 " --> pdb=" O LEU 6 48 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS 6 52 " --> pdb=" O SER 6 49 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR 6 53 " --> pdb=" O SER 6 50 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS 6 55 " --> pdb=" O LYS 6 52 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN 6 57 " --> pdb=" O ILE 6 54 " (cutoff:3.500A) Processing helix chain '6' and resid 73 through 94 removed outlier: 3.502A pdb=" N LEU 6 79 " --> pdb=" O ALA 6 75 " (cutoff:3.500A) Processing helix chain '6' and resid 99 through 103 Processing helix chain '6' and resid 105 through 119 removed outlier: 3.677A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 130 Processing helix chain '6' and resid 134 through 137 No H-bonds generated for 'chain '6' and resid 134 through 137' Processing helix chain '7' and resid 84 through 104 removed outlier: 3.643A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 110 through 113 Processing helix chain '7' and resid 116 through 119 No H-bonds generated for 'chain '7' and resid 116 through 119' Processing helix chain '7' and resid 124 through 144 removed outlier: 3.562A pdb=" N TYR 7 137 " --> pdb=" O ALA 7 133 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR 7 138 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS 7 139 " --> pdb=" O ASP 7 135 " (cutoff:3.500A) Processing helix chain '7' and resid 147 through 162 removed outlier: 3.505A pdb=" N LEU 7 150 " --> pdb=" O PHE 7 147 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER 7 151 " --> pdb=" O ASP 7 148 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA 7 154 " --> pdb=" O SER 7 151 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER 7 155 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL 7 158 " --> pdb=" O SER 7 155 " (cutoff:3.500A) Proline residue: 7 159 - end of helix removed outlier: 3.887A pdb=" N ALA 7 162 " --> pdb=" O PRO 7 159 " (cutoff:3.500A) Processing helix chain '7' and resid 175 through 186 removed outlier: 3.578A pdb=" N ASN 7 184 " --> pdb=" O GLY 7 180 " (cutoff:3.500A) 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 36 Processing helix chain '8' and resid 40 through 43 No H-bonds generated for 'chain '8' and resid 40 through 43' Processing helix chain '8' and resid 45 through 79 removed outlier: 3.824A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA 8 79 " --> pdb=" O GLU 8 75 " (cutoff:3.500A) Processing helix chain '9' and resid 5 through 16 removed outlier: 3.863A pdb=" N LYS 9 9 " --> pdb=" O SER 9 5 " (cutoff:3.500A) Processing helix chain '9' and resid 20 through 23 No H-bonds generated for 'chain '9' and resid 20 through 23' Processing helix chain '9' and resid 34 through 56 removed outlier: 3.516A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN 9 50 " --> pdb=" O MET 9 46 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN 9 56 " --> pdb=" O LEU 9 52 " (cutoff:3.500A) Processing helix chain '9' and resid 77 through 79 No H-bonds generated for 'chain '9' and resid 77 through 79' Processing helix chain '9' and resid 83 through 94 removed outlier: 3.657A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 91 removed outlier: 3.909A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 125 removed outlier: 5.067A pdb=" N LYS A 97 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 100 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 104 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 105 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 107 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 109 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 110 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER A 112 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER A 117 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 119 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 121 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE A 122 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A 125 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.637A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 125 removed outlier: 5.113A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL B 100 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 104 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 105 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 107 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 111 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 115 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 118 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU B 119 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 121 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 124 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU B 125 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 91 removed outlier: 4.172A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 124 removed outlier: 3.587A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 3.944A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 125 removed outlier: 3.651A pdb=" N ALA D 96 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 105 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE D 107 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR D 110 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU D 111 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 118 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 120 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 122 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 91 removed outlier: 4.229A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 125 removed outlier: 3.581A pdb=" N ALA E 96 " --> pdb=" O PRO E 93 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 99 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL E 100 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU E 104 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU E 105 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE E 107 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU E 109 " --> pdb=" O GLY E 106 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU E 111 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER E 112 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA E 114 " --> pdb=" O GLU E 111 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER E 117 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 118 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL E 120 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU E 125 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 91 removed outlier: 4.003A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 124 removed outlier: 4.701A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU F 104 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU F 105 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE F 107 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR F 110 " --> pdb=" O PHE F 107 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER F 117 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU F 118 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 119 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL F 121 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 124 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 91 removed outlier: 3.990A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 110 removed outlier: 3.610A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU G 99 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL G 100 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU G 105 " --> pdb=" O TYR G 102 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE G 107 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR G 110 " --> pdb=" O PHE G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 125 Processing helix chain 'H' and resid 55 through 91 removed outlier: 3.788A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 5.322A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU H 99 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL H 100 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA H 103 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU H 104 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA H 108 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR H 110 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER H 117 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL H 121 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE H 122 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE H 124 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 65 removed outlier: 3.592A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 91 removed outlier: 3.690A pdb=" N GLY I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL I 74 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU I 78 " --> pdb=" O GLY I 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY I 79 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET I 81 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE I 82 " --> pdb=" O GLY I 79 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU I 85 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA I 89 " --> pdb=" O ILE I 86 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG I 91 " --> pdb=" O GLY I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 126 removed outlier: 3.675A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU I 104 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU I 105 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE I 107 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU I 111 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU I 115 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU I 118 " --> pdb=" O LEU I 115 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU I 119 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL I 121 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE I 124 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU I 125 " --> pdb=" O PHE I 122 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE I 126 " --> pdb=" O LEU I 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 91 removed outlier: 4.023A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 125 removed outlier: 3.567A pdb=" N GLY J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 118 Processing helix chain 'M' and resid 135 through 141 Processing helix chain 'M' and resid 148 through 163 removed outlier: 3.534A pdb=" N THR M 153 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 176 No H-bonds generated for 'chain 'M' and resid 174 through 176' Processing helix chain 'M' and resid 178 through 199 removed outlier: 3.655A pdb=" N SER M 187 " --> pdb=" O GLY M 183 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 263 removed outlier: 3.864A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA M 260 " --> pdb=" O GLY M 256 " (cutoff:3.500A) removed outlier: 3.673A 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 310 removed outlier: 3.529A pdb=" N GLY M 276 " --> pdb=" O PRO M 272 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE M 310 " --> pdb=" O TYR M 306 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 Processing helix chain 'P' and resid 67 through 83 removed outlier: 4.046A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU P 74 " --> pdb=" O VAL P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 92 No H-bonds generated for 'chain 'P' and resid 89 through 92' Processing helix chain 'P' and resid 98 through 108 removed outlier: 3.685A pdb=" N THR P 102 " --> pdb=" O THR P 98 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 127 removed outlier: 4.055A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 148 removed outlier: 3.912A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL P 137 " --> pdb=" O LEU P 134 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 176 removed outlier: 4.459A pdb=" N LYS P 176 " --> pdb=" O LYS P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 228 removed outlier: 3.507A pdb=" N LYS P 224 " --> pdb=" O ASN P 220 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU P 227 " --> pdb=" O ASN P 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 12 No H-bonds generated for 'chain 'Q' and resid 10 through 12' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 4.355A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 38 removed outlier: 3.511A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 33 through 38' Processing helix chain 'R' and resid 30 through 37 removed outlier: 3.799A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 157 through 167 removed outlier: 3.558A pdb=" N LYS R 161 " --> pdb=" O PRO R 157 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 195 removed outlier: 3.573A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 70 removed outlier: 3.708A pdb=" N ASN S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 78 Processing helix chain 'S' and resid 83 through 88 Processing helix chain 'S' and resid 116 through 130 removed outlier: 3.681A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR S 130 " --> pdb=" O THR S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 147 No H-bonds generated for 'chain 'S' and resid 144 through 147' Processing helix chain 'S' and resid 172 through 184 removed outlier: 3.635A pdb=" N LEU S 182 " --> pdb=" O ILE S 178 " (cutoff:3.500A) 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 273 removed outlier: 3.898A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) Processing helix chain 'S' and resid 275 through 278 No H-bonds generated for 'chain 'S' and resid 275 through 278' Processing helix chain 'S' and resid 280 through 312 removed outlier: 3.953A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 75 Proline residue: T 68 - end of helix removed outlier: 3.592A pdb=" N LYS T 71 " --> pdb=" O ILE T 67 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 207 through 212 Processing helix chain 'T' and resid 231 through 246 removed outlier: 3.512A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) Processing helix chain 'T' and resid 267 through 279 removed outlier: 3.711A pdb=" N LEU T 272 " --> pdb=" O THR T 268 " (cutoff:3.500A) 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: 4.343A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.756A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA T 333 " --> pdb=" O LYS T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 352 through 364 removed outlier: 4.305A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR T 356 " --> pdb=" O ASP T 353 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU T 361 " --> pdb=" O HIS T 358 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU T 363 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 Processing helix chain 'T' and resid 410 through 414 Processing helix chain 'T' and resid 431 through 434 removed outlier: 3.660A 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 443 through 455 removed outlier: 3.744A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) Processing helix chain 'T' and resid 459 through 461 No H-bonds generated for 'chain 'T' and resid 459 through 461' Processing helix chain 'T' and resid 471 through 480 Processing helix chain 'T' and resid 494 through 505 removed outlier: 3.808A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 520 No H-bonds generated for 'chain 'T' and resid 517 through 520' Processing helix chain 'T' and resid 523 through 527 Processing helix chain 'T' and resid 531 through 539 Processing helix chain 'T' and resid 544 through 555 removed outlier: 4.078A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG T 555 " --> pdb=" O LYS T 551 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 49 removed outlier: 3.960A pdb=" N LEU U 48 " --> pdb=" O ALA U 44 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG U 49 " --> pdb=" O LEU U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 73 removed outlier: 3.724A pdb=" N SER U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix removed outlier: 3.609A pdb=" N GLU U 72 " --> pdb=" O PRO U 68 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 157 through 159 No H-bonds generated for 'chain 'U' and resid 157 through 159' Processing helix chain 'U' and resid 207 through 212 Processing helix chain 'U' and resid 231 through 246 removed outlier: 3.515A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS U 243 " --> pdb=" O ILE U 239 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN U 244 " --> pdb=" O ILE U 240 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 279 removed outlier: 3.659A pdb=" N LEU U 275 " --> pdb=" O GLN U 271 " (cutoff:3.500A) Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 316 Proline residue: U 303 - end of helix removed outlier: 3.531A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 330 through 340 Processing helix chain 'U' and resid 347 through 349 No H-bonds generated for 'chain 'U' and resid 347 through 349' Processing helix chain 'U' and resid 352 through 364 removed outlier: 4.317A pdb=" N PHE U 355 " --> pdb=" O GLY U 352 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU U 357 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER U 359 " --> pdb=" O TYR U 356 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG U 360 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU U 362 " --> pdb=" O SER U 359 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU U 363 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 370 through 372 No H-bonds generated for 'chain 'U' and resid 370 through 372' Processing helix chain 'U' and resid 393 through 401 Processing helix chain 'U' and resid 410 through 414 removed outlier: 3.622A pdb=" N TYR U 414 " --> pdb=" O THR U 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 410 through 414' Processing helix chain 'U' and resid 437 through 442 removed outlier: 3.557A pdb=" N GLN U 441 " --> pdb=" O PRO U 437 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 437 through 442' Processing helix chain 'U' and resid 444 through 454 removed outlier: 3.704A pdb=" N LEU U 448 " --> pdb=" O GLY U 444 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU U 449 " --> pdb=" O THR U 445 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA U 451 " --> pdb=" O LYS U 447 " (cutoff:3.500A) Processing helix chain 'U' and resid 457 through 459 No H-bonds generated for 'chain 'U' and resid 457 through 459' Processing helix chain 'U' and resid 466 through 468 No H-bonds generated for 'chain 'U' and resid 466 through 468' Processing helix chain 'U' and resid 472 through 484 removed outlier: 3.575A pdb=" N ARG U 479 " --> pdb=" O GLU U 475 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU U 482 " --> pdb=" O ALA U 478 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET U 483 " --> pdb=" O ARG U 479 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 500 removed outlier: 3.520A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 502 through 505 No H-bonds generated for 'chain 'U' and resid 502 through 505' Processing helix chain 'U' and resid 520 through 526 Processing helix chain 'U' and resid 531 through 539 Processing helix chain 'U' and resid 544 through 553 removed outlier: 3.563A pdb=" N ALA U 548 " --> pdb=" O PRO U 544 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 66 removed outlier: 3.574A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 212 Processing helix chain 'V' and resid 231 through 246 Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 284 Processing helix chain 'V' and resid 296 through 314 Proline residue: V 303 - end of helix removed outlier: 4.502A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 328 through 340 removed outlier: 3.558A pdb=" N ALA V 333 " --> pdb=" O LYS V 329 " (cutoff:3.500A) Processing helix chain 'V' and resid 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.294A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR V 356 " --> pdb=" O ASP V 353 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER V 359 " --> pdb=" O TYR V 356 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU V 362 " --> pdb=" O SER V 359 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG V 364 " --> pdb=" O LEU V 361 " (cutoff:3.500A) Processing helix chain 'V' and resid 370 through 372 No H-bonds generated for 'chain 'V' and resid 370 through 372' Processing helix chain 'V' and resid 393 through 399 Processing helix chain 'V' and resid 410 through 414 removed outlier: 3.548A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 410 through 414' Processing helix chain 'V' and resid 439 through 456 removed outlier: 3.634A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN V 452 " --> pdb=" O LEU V 448 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL V 456 " --> pdb=" O GLN V 452 " (cutoff:3.500A) Processing helix chain 'V' and resid 471 through 484 removed outlier: 3.697A pdb=" N ALA V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 505 removed outlier: 3.831A pdb=" N VAL V 499 " --> pdb=" O GLU V 495 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA V 500 " --> pdb=" O ARG V 496 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) Processing helix chain 'V' and resid 514 through 527 removed outlier: 3.941A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL V 518 " --> pdb=" O GLN V 515 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA V 519 " --> pdb=" O ASP V 516 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU V 521 " --> pdb=" O VAL V 518 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU V 522 " --> pdb=" O ALA V 519 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE V 525 " --> pdb=" O GLU V 522 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER V 526 " --> pdb=" O ALA V 523 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 539 Processing helix chain 'V' and resid 546 through 554 Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 167 through 170 No H-bonds generated for 'chain 'X' and resid 167 through 170' Processing helix chain 'X' and resid 189 through 200 Processing helix chain 'X' and resid 217 through 229 Processing helix chain 'X' and resid 236 through 241 removed outlier: 4.812A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 258 No H-bonds generated for 'chain 'X' and resid 255 through 258' Processing helix chain 'X' and resid 261 through 274 Processing helix chain 'X' and resid 288 through 296 Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.193A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 344 No H-bonds generated for 'chain 'X' and resid 342 through 344' Processing helix chain 'X' and resid 349 through 357 removed outlier: 3.707A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE X 355 " --> pdb=" O PRO X 351 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA X 356 " --> pdb=" O ALA X 352 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N HIS X 357 " --> pdb=" O THR X 353 " (cutoff:3.500A) Processing helix chain 'X' and resid 366 through 371 removed outlier: 3.794A pdb=" N LEU X 371 " --> pdb=" O SER X 367 " (cutoff:3.500A) Processing helix chain 'X' and resid 389 through 392 No H-bonds generated for 'chain 'X' and resid 389 through 392' Processing helix chain 'X' and resid 394 through 417 removed outlier: 3.554A pdb=" N ASN X 398 " --> pdb=" O ALA X 394 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 429 through 443 removed outlier: 3.589A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 451 through 454 No H-bonds generated for 'chain 'X' and resid 451 through 454' Processing helix chain 'X' and resid 463 through 475 removed outlier: 3.682A pdb=" N GLY X 469 " --> pdb=" O ASP X 465 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL X 473 " --> pdb=" O GLY X 469 " (cutoff:3.500A) Processing helix chain 'X' and resid 492 through 504 removed outlier: 3.960A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP X 500 " --> pdb=" O LYS X 496 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA X 503 " --> pdb=" O ALA X 499 " (cutoff:3.500A) Processing helix chain 'X' and resid 520 through 523 No H-bonds generated for 'chain 'X' and resid 520 through 523' Processing helix chain 'X' and resid 527 through 532 Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 189 through 203 removed outlier: 3.568A pdb=" N MET Y 194 " --> pdb=" O THR Y 190 " (cutoff:3.500A) Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 3.729A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 274 removed outlier: 5.032A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 300 Processing helix chain 'Y' and resid 314 through 322 removed outlier: 3.548A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 344 No H-bonds generated for 'chain 'Y' and resid 342 through 344' Processing helix chain 'Y' and resid 349 through 355 Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 389 through 411 removed outlier: 7.400A pdb=" N ALA Y 394 " --> pdb=" O ASN Y 390 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU Y 395 " --> pdb=" O VAL Y 391 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS Y 396 " --> pdb=" O ILE Y 392 " (cutoff:3.500A) Processing helix chain 'Y' and resid 414 through 419 removed outlier: 3.840A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 427 through 442 removed outlier: 4.545A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL Y 433 " --> pdb=" O ASP Y 429 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing helix chain 'Y' and resid 451 through 454 No H-bonds generated for 'chain 'Y' and resid 451 through 454' Processing helix chain 'Y' and resid 463 through 475 removed outlier: 3.563A pdb=" N SER Y 468 " --> pdb=" O ALA Y 464 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 492 through 507 removed outlier: 3.819A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU Y 497 " --> pdb=" O LYS Y 493 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP Y 505 " --> pdb=" O LYS Y 501 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE Y 506 " --> pdb=" O MET Y 502 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA Y 507 " --> pdb=" O ALA Y 503 " (cutoff:3.500A) Processing helix chain 'Y' and resid 527 through 530 No H-bonds generated for 'chain 'Y' and resid 527 through 530' Processing helix chain 'Y' and resid 545 through 553 removed outlier: 3.558A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU Y 552 " --> pdb=" O ASP Y 548 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 150 through 152 No H-bonds generated for 'chain 'Z' and resid 150 through 152' Processing helix chain 'Z' and resid 165 through 170 Processing helix chain 'Z' and resid 191 through 200 Processing helix chain 'Z' and resid 217 through 229 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 4.666A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 4.974A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 293 removed outlier: 3.801A pdb=" N GLN Z 292 " --> pdb=" O ARG Z 289 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA Z 293 " --> pdb=" O PHE Z 290 " (cutoff:3.500A) Processing helix chain 'Z' and resid 295 through 298 No H-bonds generated for 'chain 'Z' and resid 295 through 298' Processing helix chain 'Z' and resid 314 through 324 removed outlier: 4.204A pdb=" N ARG Z 324 " --> pdb=" O GLY Z 320 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 357 removed outlier: 3.555A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA Z 356 " --> pdb=" O ALA Z 352 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N HIS Z 357 " --> pdb=" O THR Z 353 " (cutoff:3.500A) Processing helix chain 'Z' and resid 366 through 371 removed outlier: 3.548A pdb=" N LEU Z 371 " --> pdb=" O SER Z 367 " (cutoff:3.500A) Processing helix chain 'Z' and resid 389 through 392 No H-bonds generated for 'chain 'Z' and resid 389 through 392' Processing helix chain 'Z' and resid 394 through 412 removed outlier: 3.548A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 420 Processing helix chain 'Z' and resid 422 through 424 No H-bonds generated for 'chain 'Z' and resid 422 through 424' Processing helix chain 'Z' and resid 430 through 442 removed outlier: 3.824A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 451 through 454 No H-bonds generated for 'chain 'Z' and resid 451 through 454' Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.597A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU Z 474 " --> pdb=" O PHE Z 470 " (cutoff:3.500A) Processing helix chain 'Z' and resid 492 through 499 removed outlier: 3.884A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) Processing helix chain 'Z' and resid 501 through 510 removed outlier: 3.803A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG Z 509 " --> pdb=" O ASP Z 505 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LYS Z 510 " --> pdb=" O ILE Z 506 " (cutoff:3.500A) Processing helix chain 'Z' and resid 528 through 532 removed outlier: 3.524A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 528 through 532' Processing sheet with id= A, first strand: chain '2' and resid 368 through 372 removed outlier: 4.287A pdb=" N ILE 2 368 " --> pdb=" O VAL 2 379 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '7' and resid 36 through 41 Processing sheet with id= C, first strand: chain 'P' and resid 188 through 190 removed outlier: 6.088A pdb=" N VAL P 156 " --> pdb=" O LYS P 189 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE P 198 " --> pdb=" O MET P 209 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'Q' and resid 45 through 48 Processing sheet with id= E, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.935A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'R' and resid 96 through 100 removed outlier: 6.701A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'S' and resid 203 through 211 removed outlier: 3.536A pdb=" N SER S 189 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'T' and resid 84 through 86 removed outlier: 4.015A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS T 116 " --> pdb=" O PHE T 132 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY T 128 " --> pdb=" O LEU T 120 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU T 122 " --> pdb=" O HIS T 126 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N HIS T 126 " --> pdb=" O LEU T 122 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR T 98 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL T 87 " --> pdb=" O TYR T 98 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= J, first strand: chain 'T' and resid 163 through 165 removed outlier: 8.089A pdb=" N THR T 164 " --> pdb=" O THR T 285 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N MET T 287 " --> pdb=" O THR T 164 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN T 264 " --> pdb=" O ASP T 325 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE T 380 " --> pdb=" O TYR T 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'T' and resid 404 through 408 Processing sheet with id= L, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.734A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= N, first strand: chain 'U' and resid 404 through 408 Processing sheet with id= O, first strand: chain 'U' and resid 285 through 290 removed outlier: 8.615A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'V' and resid 84 through 86 removed outlier: 6.376A pdb=" N GLY V 128 " --> pdb=" O LEU V 120 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU V 122 " --> pdb=" O HIS V 126 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N HIS V 126 " --> pdb=" O LEU V 122 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR V 98 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL V 87 " --> pdb=" O TYR V 98 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= R, first strand: chain 'V' and resid 404 through 408 Processing sheet with id= S, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.713A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'X' and resid 38 through 44 removed outlier: 6.378A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU X 72 " --> pdb=" O VAL X 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.749A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE X 207 " --> pdb=" O LEU X 281 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE X 283 " --> pdb=" O PHE X 207 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL X 209 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP X 285 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA X 211 " --> pdb=" O ASP X 285 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= W, first strand: chain 'Y' and resid 39 through 44 removed outlier: 6.318A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Y' and resid 110 through 113 removed outlier: 3.523A pdb=" N ASP Y 139 " --> pdb=" O VAL Y 113 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Y' and resid 244 through 250 removed outlier: 6.770A pdb=" N SER Y 208 " --> pdb=" O THR Y 245 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL Y 247 " --> pdb=" O SER Y 208 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE Y 210 " --> pdb=" O VAL Y 247 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLY Y 249 " --> pdb=" O PHE Y 210 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLY Y 212 " --> pdb=" O GLY Y 249 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N VAL Y 209 " --> pdb=" O ASP Y 279 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU Y 281 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA Y 211 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE Y 283 " --> pdb=" O ALA Y 211 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL Y 213 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 213 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLU Y 215 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER Y 332 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU Y 282 " --> pdb=" O SER Y 332 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR Y 334 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL Y 284 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 284 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLY Y 180 " --> pdb=" O ASP Y 359 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR Y 361 " --> pdb=" O GLY Y 180 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE Y 182 " --> pdb=" O THR Y 361 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL Y 363 " --> pdb=" O PHE Y 182 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Z' and resid 37 through 39 removed outlier: 4.891A pdb=" N LEU Z 72 " --> pdb=" O VAL Z 65 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG Z 86 " --> pdb=" O ALA Z 77 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N HIS Z 79 " --> pdb=" O THR Z 84 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR Z 84 " --> pdb=" O HIS Z 79 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ARG Z 51 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL Z 40 " --> pdb=" O ARG Z 51 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= AB, first strand: chain 'Z' and resid 360 through 363 removed outlier: 7.366A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLY Z 183 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL Z 339 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE Z 207 " --> pdb=" O LEU Z 281 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N PHE Z 283 " --> pdb=" O PHE Z 207 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL Z 209 " --> pdb=" O PHE Z 283 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP Z 285 " --> pdb=" O VAL Z 209 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA Z 211 " --> pdb=" O ASP Z 285 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Z' and resid 559 through 561 2207 hydrogen bonds defined for protein. 6057 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: 16.01 Time building geometry restraints manager: 17.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14096 1.33 - 1.45: 9547 1.45 - 1.57: 30776 1.57 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54694 Sorted by residual: bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.91e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.89e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.39e+01 bond pdb=" C5 ATP V1001 " pdb=" N7 ATP V1001 " ideal model delta sigma weight residual 1.387 1.330 0.057 1.00e-02 1.00e+04 3.25e+01 ... (remaining 54689 not shown) Histogram of bond angle deviations from ideal: 96.78 - 104.61: 868 104.61 - 112.45: 28212 112.45 - 120.28: 24258 120.28 - 128.11: 20490 128.11 - 135.94: 344 Bond angle restraints: 74172 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 123.81 16.06 1.00e+00 1.00e+00 2.58e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 124.81 15.06 1.00e+00 1.00e+00 2.27e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 122.95 13.88 1.00e+00 1.00e+00 1.93e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 126.96 12.91 1.00e+00 1.00e+00 1.67e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 124.78 12.05 1.00e+00 1.00e+00 1.45e+02 ... (remaining 74167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 32457 35.96 - 71.91: 531 71.91 - 107.87: 38 107.87 - 143.83: 1 143.83 - 179.78: 3 Dihedral angle restraints: 33030 sinusoidal: 12669 harmonic: 20361 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -124.45 -55.55 0 5.00e+00 4.00e-02 1.23e+02 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 -127.26 -52.74 0 5.00e+00 4.00e-02 1.11e+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 -129.04 -50.96 0 5.00e+00 4.00e-02 1.04e+02 ... (remaining 33027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 7182 0.078 - 0.155: 1363 0.155 - 0.233: 127 0.233 - 0.311: 14 0.311 - 0.388: 4 Chirality restraints: 8690 Sorted by residual: chirality pdb=" CB VAL V 180 " pdb=" CA VAL V 180 " pdb=" CG1 VAL V 180 " pdb=" CG2 VAL V 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.77e+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 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CB VAL U 81 " pdb=" CA VAL U 81 " pdb=" CG1 VAL U 81 " pdb=" CG2 VAL U 81 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 8687 not shown) Planarity restraints: 9512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.032 2.00e-02 2.50e+03 6.33e-02 4.01e+01 pdb=" C ALA Z 503 " -0.110 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.041 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU M 261 " 0.064 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO M 262 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO M 262 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO M 262 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR 1 92 " -0.057 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO 1 93 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO 1 93 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO 1 93 " -0.047 5.00e-02 4.00e+02 ... (remaining 9509 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 15 2.13 - 2.82: 17583 2.82 - 3.51: 70083 3.51 - 4.21: 139207 4.21 - 4.90: 234918 Nonbonded interactions: 461806 Sorted by model distance: nonbonded pdb=" CD2 LEU P 37 " pdb=" NE1 TRP V 73 " model vdw 1.436 3.540 nonbonded pdb=" O ASP T 467 " pdb=" N ALA T 469 " model vdw 1.499 2.520 nonbonded pdb=" OE1 GLU M 288 " pdb=" O HOH M 701 " model vdw 1.660 2.440 nonbonded pdb=" O GLN Q 49 " pdb=" O SER Q 60 " model vdw 1.937 3.040 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.038 2.170 ... (remaining 461801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 36 through 556) selection = chain 'Y' selection = (chain 'Z' and resid 36 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 23.330 Check model and map are aligned: 0.580 Set scattering table: 0.360 Process input model: 113.000 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.134 54694 Z= 0.694 Angle : 0.980 16.061 74172 Z= 0.559 Chirality : 0.061 0.388 8690 Planarity : 0.007 0.097 9512 Dihedral : 14.360 179.785 19942 Min Nonbonded Distance : 1.436 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.67 % Favored : 95.11 % Rotamer: Outliers : 0.48 % Allowed : 5.45 % Favored : 94.07 % 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: -5.14 (0.07), residues: 7039 helix: -4.37 (0.04), residues: 3763 sheet: -1.41 (0.19), residues: 629 loop : -2.02 (0.10), residues: 2647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP Z 141 HIS 0.012 0.002 HIS 7 123 PHE 0.035 0.003 PHE S 249 TYR 0.025 0.003 TYR 7 119 ARG 0.014 0.001 ARG 3 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 883 time to evaluate : 4.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 109 LYS cc_start: 0.8624 (tptt) cc_final: 0.8355 (tppt) REVERT: 1 283 ASP cc_start: 0.8474 (m-30) cc_final: 0.8256 (m-30) REVERT: 1 604 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7357 (mtm-85) REVERT: 1 613 ASP cc_start: 0.8096 (m-30) cc_final: 0.7850 (m-30) REVERT: 2 131 LYS cc_start: 0.7744 (mppt) cc_final: 0.7335 (ptpt) REVERT: 2 154 ASP cc_start: 0.6538 (t0) cc_final: 0.5682 (p0) REVERT: 3 151 ASN cc_start: 0.7495 (t0) cc_final: 0.7192 (t0) REVERT: 4 133 ASP cc_start: 0.8248 (t0) cc_final: 0.7955 (t0) REVERT: 4 271 ASP cc_start: 0.7985 (m-30) cc_final: 0.7686 (m-30) REVERT: 5 54 LYS cc_start: 0.8965 (tttt) cc_final: 0.8736 (tttp) REVERT: 5 115 ILE cc_start: 0.9115 (tp) cc_final: 0.8660 (tp) REVERT: 6 37 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8118 (ttmt) REVERT: 7 24 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7481 (tp40) REVERT: 7 129 LYS cc_start: 0.8414 (mttt) cc_final: 0.8128 (mtpt) REVERT: 8 39 LYS cc_start: 0.8818 (tttm) cc_final: 0.8609 (tttp) REVERT: 8 69 LYS cc_start: 0.8154 (mttt) cc_final: 0.5945 (tmtt) REVERT: B 81 MET cc_start: 0.8815 (ttp) cc_final: 0.8195 (tmm) REVERT: B 82 PHE cc_start: 0.8846 (m-80) cc_final: 0.8596 (m-80) REVERT: C 92 ASN cc_start: 0.8701 (t0) cc_final: 0.8414 (t0) REVERT: C 95 ILE cc_start: 0.9017 (pt) cc_final: 0.8483 (pt) REVERT: H 61 MET cc_start: 0.7608 (mmp) cc_final: 0.7333 (mmm) REVERT: J 81 MET cc_start: 0.7403 (ttp) cc_final: 0.7117 (ttp) REVERT: M 168 MET cc_start: 0.8156 (mmp) cc_final: 0.7887 (mmt) REVERT: M 230 THR cc_start: 0.9128 (t) cc_final: 0.8887 (m) REVERT: M 324 LYS cc_start: 0.6917 (tptt) cc_final: 0.6567 (tmtt) REVERT: P 73 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: P 136 GLU cc_start: 0.8245 (mp0) cc_final: 0.7661 (mp0) REVERT: Q 10 ARG cc_start: 0.8098 (tpp-160) cc_final: 0.7602 (mmt180) REVERT: Q 52 TYR cc_start: 0.7597 (m-80) cc_final: 0.7284 (m-80) REVERT: S 109 LYS cc_start: 0.8386 (pttt) cc_final: 0.8097 (pttp) REVERT: S 153 ILE cc_start: 0.7632 (tt) cc_final: 0.7171 (tt) REVERT: S 240 SER cc_start: 0.8936 (m) cc_final: 0.8477 (p) REVERT: S 244 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7480 (ttp80) REVERT: T 49 ARG cc_start: 0.8428 (mtp-110) cc_final: 0.7894 (mtp85) REVERT: T 447 LYS cc_start: 0.8498 (ptpt) cc_final: 0.8234 (ptpp) REVERT: T 448 LEU cc_start: 0.8772 (tp) cc_final: 0.8528 (tp) REVERT: T 479 ARG cc_start: 0.6691 (mmp-170) cc_final: 0.5157 (tpt170) REVERT: T 525 ILE cc_start: 0.8466 (pt) cc_final: 0.8242 (mm) REVERT: U 74 GLU cc_start: 0.8170 (pp20) cc_final: 0.7874 (pm20) REVERT: U 75 LYS cc_start: 0.8277 (mmpt) cc_final: 0.7506 (mttp) REVERT: U 496 ARG cc_start: 0.8675 (mtt180) cc_final: 0.8437 (mtt-85) REVERT: U 515 GLN cc_start: 0.8126 (mp10) cc_final: 0.7921 (mp10) REVERT: V 287 MET cc_start: 0.8547 (tpt) cc_final: 0.8223 (tpt) REVERT: V 471 GLN cc_start: 0.6782 (tp40) cc_final: 0.6432 (tp40) REVERT: X 168 ASP cc_start: 0.8455 (m-30) cc_final: 0.8016 (m-30) REVERT: X 386 MET cc_start: 0.8654 (mmm) cc_final: 0.8348 (mmm) REVERT: X 411 LYS cc_start: 0.8666 (tttt) cc_final: 0.8440 (mmmt) REVERT: Y 194 MET cc_start: 0.8981 (mtm) cc_final: 0.8778 (mtp) REVERT: Y 422 MET cc_start: 0.6434 (tpt) cc_final: 0.6214 (mmm) REVERT: Y 441 ARG cc_start: 0.8554 (mmt-90) cc_final: 0.8244 (mpt180) REVERT: Z 49 ASP cc_start: 0.8040 (m-30) cc_final: 0.7732 (m-30) REVERT: Z 82 ASP cc_start: 0.7676 (t0) cc_final: 0.7317 (t0) REVERT: Z 226 GLU cc_start: 0.7412 (tp30) cc_final: 0.7136 (tp30) REVERT: Z 502 MET cc_start: 0.8089 (mtp) cc_final: 0.7650 (mtp) outliers start: 27 outliers final: 14 residues processed: 908 average time/residue: 0.5722 time to fit residues: 838.1262 Evaluate side-chains 629 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 614 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain P residue 73 GLU Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain Z residue 399 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 8.9990 chunk 529 optimal weight: 0.6980 chunk 293 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 356 optimal weight: 3.9990 chunk 282 optimal weight: 0.6980 chunk 547 optimal weight: 0.8980 chunk 211 optimal weight: 0.5980 chunk 332 optimal weight: 0.2980 chunk 407 optimal weight: 0.6980 chunk 633 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 0 60 GLN 0 61 HIS 1 48 ASN 1 257 HIS 1 285 GLN 1 316 ASN 1 482 ASN 1 531 HIS 1 587 ASN 1 590 HIS ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 243 GLN 2 289 HIS 3 206 ASN 4 135 ASN 4 240 GLN 5 107 ASN 6 40 ASN 6 74 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 86 HIS 7 123 HIS 7 170 HIS 7 184 ASN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 35 GLN F 92 ASN F 98 GLN G 92 ASN G 98 GLN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN M 108 ASN M 163 ASN P 52 GLN P 66 GLN P 223 ASN R 73 ASN R 85 GLN R 137 HIS ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 257 ASN S 262 ASN T 64 GLN T 134 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 386 GLN T 435 GLN U 60 GLN U 78 GLN U 179 ASN U 242 GLN U 319 HIS U 497 GLN U 539 ASN V 64 GLN V 123 GLN V 139 HIS V 152 ASN V 196 GLN V 241 HIS V 242 GLN V 386 GLN V 435 GLN V 461 GLN V 486 GLN V 497 GLN X 204 HIS Y 199 ASN Y 278 GLN Y 286 ASN Y 294 ASN Z 42 GLN Z 199 ASN Z 337 GLN ** Z 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 54694 Z= 0.178 Angle : 0.576 11.357 74172 Z= 0.301 Chirality : 0.042 0.170 8690 Planarity : 0.005 0.068 9512 Dihedral : 7.397 173.313 7690 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.14 % Favored : 96.73 % Rotamer: Outliers : 1.46 % Allowed : 9.30 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.09), residues: 7039 helix: -2.36 (0.07), residues: 3789 sheet: -1.10 (0.20), residues: 632 loop : -1.49 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 9 73 HIS 0.006 0.001 HIS V 61 PHE 0.022 0.001 PHE P 221 TYR 0.025 0.001 TYR 4 211 ARG 0.006 0.000 ARG Y 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 730 time to evaluate : 4.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 109 LYS cc_start: 0.8413 (tptt) cc_final: 0.8018 (tppt) REVERT: 1 613 ASP cc_start: 0.7802 (m-30) cc_final: 0.7521 (m-30) REVERT: 2 74 ASN cc_start: 0.8549 (t0) cc_final: 0.8027 (m-40) REVERT: 2 131 LYS cc_start: 0.7641 (mppt) cc_final: 0.7184 (ptpt) REVERT: 2 154 ASP cc_start: 0.6624 (t0) cc_final: 0.5705 (p0) REVERT: 4 133 ASP cc_start: 0.8189 (t0) cc_final: 0.7878 (t0) REVERT: 4 271 ASP cc_start: 0.7991 (m-30) cc_final: 0.7599 (m-30) REVERT: 5 54 LYS cc_start: 0.8584 (tttt) cc_final: 0.8377 (tttp) REVERT: 5 115 ILE cc_start: 0.9043 (tp) cc_final: 0.8616 (tp) REVERT: 8 3 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8244 (tt) REVERT: 8 69 LYS cc_start: 0.8118 (mttt) cc_final: 0.6012 (tmtt) REVERT: 9 33 LYS cc_start: 0.8543 (tttm) cc_final: 0.8173 (tptt) REVERT: 9 56 ASN cc_start: 0.8838 (p0) cc_final: 0.8430 (p0) REVERT: A 81 MET cc_start: 0.8089 (ttp) cc_final: 0.7788 (ttp) REVERT: B 81 MET cc_start: 0.8666 (ttp) cc_final: 0.8461 (ttp) REVERT: B 97 LYS cc_start: 0.8535 (mtmm) cc_final: 0.8309 (mttm) REVERT: H 61 MET cc_start: 0.7649 (mmp) cc_final: 0.7423 (mmm) REVERT: M 168 MET cc_start: 0.8082 (mmt) cc_final: 0.7799 (mmt) REVERT: M 230 THR cc_start: 0.9232 (t) cc_final: 0.8919 (m) REVERT: M 324 LYS cc_start: 0.6979 (tptt) cc_final: 0.6491 (tmtt) REVERT: P 49 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7852 (t) REVERT: P 136 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: P 191 ASP cc_start: 0.7731 (t0) cc_final: 0.7461 (t0) REVERT: Q 10 ARG cc_start: 0.8218 (tpp-160) cc_final: 0.7625 (mmt180) REVERT: Q 52 TYR cc_start: 0.7615 (m-80) cc_final: 0.7321 (m-80) REVERT: S 109 LYS cc_start: 0.8373 (pttt) cc_final: 0.8027 (pttp) REVERT: S 240 SER cc_start: 0.8866 (m) cc_final: 0.8503 (p) REVERT: S 244 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7417 (ttp80) REVERT: T 49 ARG cc_start: 0.8368 (mtp-110) cc_final: 0.7782 (mtp85) REVERT: T 447 LYS cc_start: 0.8371 (ptpt) cc_final: 0.8119 (ptpp) REVERT: T 479 ARG cc_start: 0.6985 (mmp-170) cc_final: 0.5356 (tpt170) REVERT: T 525 ILE cc_start: 0.8469 (pt) cc_final: 0.8263 (mm) REVERT: U 46 ASP cc_start: 0.6995 (m-30) cc_final: 0.6791 (m-30) REVERT: U 74 GLU cc_start: 0.8117 (pp20) cc_final: 0.7758 (pm20) REVERT: U 496 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8388 (mtt-85) REVERT: U 539 ASN cc_start: 0.8165 (m-40) cc_final: 0.7957 (m110) REVERT: V 121 ASN cc_start: 0.8388 (m110) cc_final: 0.8180 (m-40) REVERT: V 274 LYS cc_start: 0.8676 (tmmt) cc_final: 0.8325 (ttpt) REVERT: V 471 GLN cc_start: 0.6552 (tp40) cc_final: 0.6289 (tp40) REVERT: Y 430 LYS cc_start: 0.6369 (ptmt) cc_final: 0.5804 (mtmm) REVERT: Z 49 ASP cc_start: 0.7733 (m-30) cc_final: 0.7529 (m-30) REVERT: Z 82 ASP cc_start: 0.7756 (t0) cc_final: 0.7296 (t0) REVERT: Z 266 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8419 (tt) REVERT: Z 395 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7743 (tp30) outliers start: 82 outliers final: 51 residues processed: 781 average time/residue: 0.5514 time to fit residues: 707.6305 Evaluate side-chains 690 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 635 time to evaluate : 4.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 36 THR Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 268 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 385 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 527 optimal weight: 0.0170 chunk 431 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 635 optimal weight: 7.9990 chunk 685 optimal weight: 0.9990 chunk 565 optimal weight: 4.9990 chunk 629 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 509 optimal weight: 2.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 298 GLN ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 74 ASN 4 111 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 GLN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 27 ASN F 98 GLN G 98 GLN ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN U 497 GLN X 198 ASN Y 286 ASN ** Z 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54694 Z= 0.171 Angle : 0.524 10.933 74172 Z= 0.270 Chirality : 0.041 0.191 8690 Planarity : 0.004 0.059 9512 Dihedral : 6.805 161.291 7680 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.62 % Favored : 96.26 % Rotamer: Outliers : 1.95 % Allowed : 10.78 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.09), residues: 7039 helix: -1.08 (0.08), residues: 3780 sheet: -0.91 (0.20), residues: 636 loop : -1.14 (0.12), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 9 73 HIS 0.006 0.001 HIS V 83 PHE 0.021 0.001 PHE 4 162 TYR 0.025 0.001 TYR 4 211 ARG 0.005 0.000 ARG T 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 688 time to evaluate : 4.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 109 LYS cc_start: 0.8400 (tptt) cc_final: 0.8113 (tppt) REVERT: 1 613 ASP cc_start: 0.7749 (m-30) cc_final: 0.7459 (m-30) REVERT: 2 74 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.7972 (m-40) REVERT: 2 131 LYS cc_start: 0.7625 (mppt) cc_final: 0.7210 (ptpt) REVERT: 2 154 ASP cc_start: 0.6593 (t0) cc_final: 0.5697 (p0) REVERT: 3 276 GLU cc_start: 0.8275 (tt0) cc_final: 0.7838 (tp30) REVERT: 4 133 ASP cc_start: 0.8199 (t0) cc_final: 0.7923 (t0) REVERT: 5 115 ILE cc_start: 0.9068 (tp) cc_final: 0.8628 (tp) REVERT: 8 69 LYS cc_start: 0.8052 (mttt) cc_final: 0.6009 (tmtt) REVERT: 9 33 LYS cc_start: 0.8531 (tttm) cc_final: 0.8167 (tptt) REVERT: 9 56 ASN cc_start: 0.8804 (p0) cc_final: 0.8583 (p0) REVERT: 9 80 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7625 (mm110) REVERT: A 81 MET cc_start: 0.8055 (ttp) cc_final: 0.7776 (ttp) REVERT: B 81 MET cc_start: 0.8723 (ttp) cc_final: 0.8513 (ttp) REVERT: B 97 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8110 (mmtt) REVERT: J 119 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.6583 (mt) REVERT: M 168 MET cc_start: 0.8049 (mmt) cc_final: 0.7760 (mmt) REVERT: M 230 THR cc_start: 0.9205 (t) cc_final: 0.8894 (m) REVERT: M 254 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8217 (mp) REVERT: M 324 LYS cc_start: 0.6983 (tptt) cc_final: 0.6488 (tmtt) REVERT: P 49 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7801 (t) REVERT: P 127 ASP cc_start: 0.8294 (t70) cc_final: 0.7894 (t70) REVERT: P 136 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: P 191 ASP cc_start: 0.7775 (t0) cc_final: 0.7555 (t0) REVERT: P 227 LEU cc_start: 0.8618 (mt) cc_final: 0.8391 (mt) REVERT: Q 10 ARG cc_start: 0.8247 (tpp-160) cc_final: 0.7653 (mmt180) REVERT: Q 52 TYR cc_start: 0.7599 (m-80) cc_final: 0.7384 (m-80) REVERT: S 62 MET cc_start: 0.7524 (mmm) cc_final: 0.7193 (mmm) REVERT: S 240 SER cc_start: 0.8861 (m) cc_final: 0.8494 (p) REVERT: S 244 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7423 (ttp80) REVERT: T 49 ARG cc_start: 0.8371 (mtp-110) cc_final: 0.7820 (mtp85) REVERT: T 447 LYS cc_start: 0.8402 (ptpt) cc_final: 0.8196 (ptpp) REVERT: T 475 GLU cc_start: 0.5815 (tm-30) cc_final: 0.5256 (mm-30) REVERT: T 479 ARG cc_start: 0.6924 (mmp-170) cc_final: 0.5217 (tpt170) REVERT: U 74 GLU cc_start: 0.8179 (pp20) cc_final: 0.7655 (pm20) REVERT: U 471 GLN cc_start: 0.7312 (tm-30) cc_final: 0.7112 (tm-30) REVERT: U 474 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7080 (mp) REVERT: U 476 ARG cc_start: 0.6997 (tpp80) cc_final: 0.6718 (tpp80) REVERT: U 482 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7776 (mm-30) REVERT: U 496 ARG cc_start: 0.8588 (mtt180) cc_final: 0.8352 (mtt-85) REVERT: U 539 ASN cc_start: 0.8168 (m-40) cc_final: 0.7669 (m110) REVERT: V 120 LEU cc_start: 0.9024 (tp) cc_final: 0.8784 (tp) REVERT: V 121 ASN cc_start: 0.8307 (m110) cc_final: 0.8103 (m110) REVERT: V 471 GLN cc_start: 0.6485 (tp40) cc_final: 0.6233 (tp40) REVERT: Y 422 MET cc_start: 0.6287 (mmm) cc_final: 0.6024 (mmm) REVERT: Y 430 LYS cc_start: 0.6113 (ptmt) cc_final: 0.5875 (mtmm) REVERT: Z 49 ASP cc_start: 0.7680 (m-30) cc_final: 0.7472 (m-30) REVERT: Z 82 ASP cc_start: 0.7771 (t0) cc_final: 0.7272 (t0) REVERT: Z 198 ASN cc_start: 0.8559 (t0) cc_final: 0.8256 (t0) REVERT: Z 266 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8379 (tt) outliers start: 110 outliers final: 68 residues processed: 761 average time/residue: 0.5401 time to fit residues: 681.0787 Evaluate side-chains 698 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 623 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 36 THR Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 74 ASN Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 268 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 5 residue 27 ASP Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 216 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 416 ILE Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 480 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 2.9990 chunk 477 optimal weight: 0.0270 chunk 329 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 303 optimal weight: 0.0010 chunk 426 optimal weight: 6.9990 chunk 637 optimal weight: 3.9990 chunk 674 optimal weight: 1.9990 chunk 332 optimal weight: 3.9990 chunk 603 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 overall best weight: 0.5646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 44 ASN ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 27 ASN E 98 GLN F 98 GLN G 98 GLN H 98 GLN P 52 GLN R 181 ASN S 41 GLN U 386 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 452 GLN Y 252 ASN Y 286 ASN ** Z 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 54694 Z= 0.146 Angle : 0.494 10.006 74172 Z= 0.253 Chirality : 0.040 0.216 8690 Planarity : 0.004 0.055 9512 Dihedral : 6.432 153.617 7676 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.41 % Favored : 96.48 % Rotamer: Outliers : 2.24 % Allowed : 11.52 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.10), residues: 7039 helix: -0.41 (0.08), residues: 3798 sheet: -0.76 (0.20), residues: 653 loop : -0.89 (0.12), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.005 0.001 HIS V 83 PHE 0.026 0.001 PHE I 107 TYR 0.024 0.001 TYR 4 211 ARG 0.006 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 684 time to evaluate : 4.652 Fit side-chains revert: symmetry clash REVERT: 1 216 LEU cc_start: 0.8842 (mt) cc_final: 0.8407 (tt) REVERT: 1 276 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8956 (pt) REVERT: 2 74 ASN cc_start: 0.8137 (t0) cc_final: 0.7857 (m-40) REVERT: 2 131 LYS cc_start: 0.7655 (mppt) cc_final: 0.7234 (ptpt) REVERT: 2 154 ASP cc_start: 0.6703 (t0) cc_final: 0.5683 (p0) REVERT: 3 276 GLU cc_start: 0.8225 (tt0) cc_final: 0.7947 (tp30) REVERT: 4 54 GLU cc_start: 0.8106 (pt0) cc_final: 0.7877 (pt0) REVERT: 4 133 ASP cc_start: 0.8191 (t0) cc_final: 0.7895 (t0) REVERT: 5 115 ILE cc_start: 0.9067 (tp) cc_final: 0.8621 (tp) REVERT: 8 3 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8293 (tt) REVERT: 8 69 LYS cc_start: 0.8017 (mttt) cc_final: 0.6023 (tmtt) REVERT: 9 33 LYS cc_start: 0.8546 (tttm) cc_final: 0.8191 (tptt) REVERT: 9 56 ASN cc_start: 0.8823 (p0) cc_final: 0.8567 (p0) REVERT: 9 80 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7624 (mm110) REVERT: A 81 MET cc_start: 0.8005 (ttp) cc_final: 0.7765 (ttp) REVERT: A 102 TYR cc_start: 0.7809 (m-80) cc_final: 0.7604 (m-80) REVERT: B 81 MET cc_start: 0.8724 (ttp) cc_final: 0.8514 (ttp) REVERT: J 119 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.6529 (mt) REVERT: M 168 MET cc_start: 0.8042 (mmt) cc_final: 0.7779 (mmt) REVERT: M 230 THR cc_start: 0.9202 (t) cc_final: 0.8890 (m) REVERT: M 254 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8219 (mp) REVERT: M 324 LYS cc_start: 0.6972 (tptt) cc_final: 0.6487 (tmtt) REVERT: P 49 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.7560 (t) REVERT: P 127 ASP cc_start: 0.8286 (t70) cc_final: 0.7918 (t70) REVERT: P 136 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: P 191 ASP cc_start: 0.7789 (t0) cc_final: 0.7163 (p0) REVERT: P 227 LEU cc_start: 0.8625 (mt) cc_final: 0.8380 (mt) REVERT: Q 10 ARG cc_start: 0.8239 (tpp-160) cc_final: 0.7655 (mmt180) REVERT: Q 52 TYR cc_start: 0.7426 (m-80) cc_final: 0.7085 (m-80) REVERT: S 62 MET cc_start: 0.7538 (mmm) cc_final: 0.7171 (mmm) REVERT: S 220 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7818 (mm) REVERT: S 240 SER cc_start: 0.8835 (m) cc_final: 0.8449 (p) REVERT: S 244 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7413 (ttp80) REVERT: T 49 ARG cc_start: 0.8360 (mtp-110) cc_final: 0.7803 (mtp85) REVERT: T 447 LYS cc_start: 0.8385 (ptpt) cc_final: 0.8185 (ptpp) REVERT: T 475 GLU cc_start: 0.5784 (tm-30) cc_final: 0.5273 (mm-30) REVERT: T 479 ARG cc_start: 0.6889 (mmp-170) cc_final: 0.5168 (tpt170) REVERT: U 72 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7690 (tm-30) REVERT: U 74 GLU cc_start: 0.8109 (pp20) cc_final: 0.7627 (pm20) REVERT: U 474 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6796 (mp) REVERT: U 496 ARG cc_start: 0.8557 (mtt180) cc_final: 0.8324 (mtt-85) REVERT: U 539 ASN cc_start: 0.8181 (m-40) cc_final: 0.7680 (m110) REVERT: V 52 LYS cc_start: 0.7246 (mmtm) cc_final: 0.6983 (mmtm) REVERT: V 120 LEU cc_start: 0.8953 (tp) cc_final: 0.8619 (tp) REVERT: V 121 ASN cc_start: 0.8241 (m110) cc_final: 0.7960 (m-40) REVERT: V 471 GLN cc_start: 0.6466 (tp40) cc_final: 0.6219 (tp40) REVERT: X 370 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7593 (mt-10) REVERT: X 484 MET cc_start: 0.7046 (tmm) cc_final: 0.6838 (tmm) REVERT: X 538 VAL cc_start: 0.6975 (OUTLIER) cc_final: 0.6632 (m) REVERT: Y 430 LYS cc_start: 0.6086 (ptmt) cc_final: 0.5850 (mtmm) REVERT: Z 82 ASP cc_start: 0.7736 (t0) cc_final: 0.7287 (t0) REVERT: Z 266 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8389 (tt) outliers start: 126 outliers final: 83 residues processed: 769 average time/residue: 0.5478 time to fit residues: 692.8412 Evaluate side-chains 703 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 610 time to evaluate : 4.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 36 THR Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 437 VAL Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 192 LYS Chi-restraints excluded: chain P residue 216 GLU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 474 LEU Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 416 ILE Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 530 LEU Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 480 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 0.8980 chunk 382 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 502 optimal weight: 4.9990 chunk 278 optimal weight: 0.9980 chunk 575 optimal weight: 0.7980 chunk 466 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 344 optimal weight: 2.9990 chunk 605 optimal weight: 0.7980 chunk 170 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 44 ASN ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 GLN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 50 ASN F 98 GLN G 98 GLN H 98 GLN P 83 GLN R 181 ASN T 405 GLN T 461 GLN ** Z 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 54694 Z= 0.179 Angle : 0.502 11.708 74172 Z= 0.256 Chirality : 0.041 0.224 8690 Planarity : 0.004 0.054 9512 Dihedral : 6.319 156.001 7675 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.59 % Favored : 96.29 % Rotamer: Outliers : 2.47 % Allowed : 11.81 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.10), residues: 7039 helix: -0.04 (0.09), residues: 3805 sheet: -0.71 (0.20), residues: 655 loop : -0.76 (0.12), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 73 HIS 0.009 0.001 HIS U 549 PHE 0.024 0.001 PHE I 107 TYR 0.023 0.001 TYR 4 211 ARG 0.010 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 642 time to evaluate : 4.624 Fit side-chains revert: symmetry clash REVERT: 1 39 LYS cc_start: 0.8392 (tppt) cc_final: 0.8135 (tptp) REVERT: 1 155 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7544 (tm-30) REVERT: 1 216 LEU cc_start: 0.8806 (mt) cc_final: 0.8352 (tt) REVERT: 1 276 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8941 (pt) REVERT: 1 486 ASP cc_start: 0.7451 (m-30) cc_final: 0.7170 (m-30) REVERT: 2 74 ASN cc_start: 0.8306 (t0) cc_final: 0.7851 (m-40) REVERT: 2 131 LYS cc_start: 0.7688 (mppt) cc_final: 0.7253 (ptpt) REVERT: 2 154 ASP cc_start: 0.6754 (t0) cc_final: 0.5760 (p0) REVERT: 3 276 GLU cc_start: 0.8229 (tt0) cc_final: 0.7946 (tp30) REVERT: 4 54 GLU cc_start: 0.8030 (pt0) cc_final: 0.7799 (pt0) REVERT: 4 133 ASP cc_start: 0.8186 (t0) cc_final: 0.7896 (t0) REVERT: 5 115 ILE cc_start: 0.9051 (tp) cc_final: 0.8597 (tp) REVERT: 8 3 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8243 (tt) REVERT: 8 69 LYS cc_start: 0.8025 (mttt) cc_final: 0.6033 (tmtt) REVERT: 9 1 MET cc_start: 0.2232 (ptt) cc_final: -0.0746 (mpp) REVERT: 9 33 LYS cc_start: 0.8540 (tttm) cc_final: 0.8190 (tptt) REVERT: 9 56 ASN cc_start: 0.8827 (p0) cc_final: 0.8548 (p0) REVERT: 9 80 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7703 (mm110) REVERT: A 81 MET cc_start: 0.8001 (ttp) cc_final: 0.7765 (ttp) REVERT: A 102 TYR cc_start: 0.7843 (m-80) cc_final: 0.7640 (m-80) REVERT: B 81 MET cc_start: 0.8735 (ttp) cc_final: 0.8521 (ttp) REVERT: F 61 MET cc_start: 0.8597 (mmt) cc_final: 0.8191 (mmt) REVERT: J 119 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.6496 (mt) REVERT: M 168 MET cc_start: 0.8045 (mmt) cc_final: 0.7787 (mmt) REVERT: M 230 THR cc_start: 0.9187 (t) cc_final: 0.8867 (m) REVERT: M 254 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8183 (mp) REVERT: M 324 LYS cc_start: 0.6869 (tptt) cc_final: 0.6513 (tmtt) REVERT: P 49 THR cc_start: 0.7756 (OUTLIER) cc_final: 0.7547 (t) REVERT: P 66 GLN cc_start: 0.8384 (mt0) cc_final: 0.7861 (mt0) REVERT: P 127 ASP cc_start: 0.8364 (t70) cc_final: 0.7936 (t70) REVERT: P 136 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: P 157 ILE cc_start: 0.8907 (mt) cc_final: 0.8574 (mt) REVERT: P 186 MET cc_start: 0.4218 (mmm) cc_final: 0.3388 (mmm) REVERT: P 191 ASP cc_start: 0.7793 (t0) cc_final: 0.7173 (p0) REVERT: P 227 LEU cc_start: 0.8622 (mt) cc_final: 0.8403 (mt) REVERT: Q 10 ARG cc_start: 0.8247 (tpp-160) cc_final: 0.7644 (mmt180) REVERT: S 62 MET cc_start: 0.7567 (mmm) cc_final: 0.7192 (mmm) REVERT: S 220 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7790 (mm) REVERT: S 240 SER cc_start: 0.8833 (m) cc_final: 0.8440 (p) REVERT: S 244 ARG cc_start: 0.7800 (ttm-80) cc_final: 0.7401 (ttp80) REVERT: T 49 ARG cc_start: 0.8370 (mtp-110) cc_final: 0.7811 (mtp85) REVERT: T 475 GLU cc_start: 0.5890 (tm-30) cc_final: 0.5312 (mm-30) REVERT: T 479 ARG cc_start: 0.6910 (mmp-170) cc_final: 0.5168 (tpt170) REVERT: U 72 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8080 (tm-30) REVERT: U 74 GLU cc_start: 0.8119 (pp20) cc_final: 0.7610 (pm20) REVERT: U 474 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6944 (mp) REVERT: U 496 ARG cc_start: 0.8543 (mtt180) cc_final: 0.8299 (mtt-85) REVERT: V 52 LYS cc_start: 0.7376 (mmtm) cc_final: 0.7167 (mmtm) REVERT: V 120 LEU cc_start: 0.8951 (tp) cc_final: 0.8679 (tp) REVERT: V 471 GLN cc_start: 0.6479 (tp40) cc_final: 0.6235 (tp40) REVERT: X 370 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7598 (mt-10) REVERT: X 538 VAL cc_start: 0.6985 (OUTLIER) cc_final: 0.6635 (m) REVERT: Y 430 LYS cc_start: 0.6111 (ptmt) cc_final: 0.5872 (mtmm) REVERT: Z 82 ASP cc_start: 0.7712 (t0) cc_final: 0.7298 (t0) REVERT: Z 266 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8363 (tt) outliers start: 139 outliers final: 100 residues processed: 737 average time/residue: 0.5408 time to fit residues: 658.7109 Evaluate side-chains 727 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 617 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 36 THR Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 437 VAL Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 27 ASP Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 192 LYS Chi-restraints excluded: chain P residue 216 GLU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 474 LEU Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 416 ILE Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 530 LEU Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 297 VAL Chi-restraints excluded: chain Z residue 480 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 226 optimal weight: 0.9990 chunk 607 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 396 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 675 optimal weight: 0.5980 chunk 560 optimal weight: 0.9980 chunk 312 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 223 optimal weight: 7.9990 chunk 354 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 44 ASN ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 189 HIS 3 229 ASN 5 59 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 GLN 8 26 HIS 8 78 HIS F 98 GLN G 98 GLN H 98 GLN P 83 GLN P 187 GLN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN U 134 ASN V 121 ASN Z 78 GLN Z 198 ASN ** Z 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 54694 Z= 0.177 Angle : 0.504 14.320 74172 Z= 0.256 Chirality : 0.041 0.235 8690 Planarity : 0.004 0.055 9512 Dihedral : 6.233 160.889 7675 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.54 % Favored : 96.35 % Rotamer: Outliers : 2.52 % Allowed : 12.45 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.10), residues: 7039 helix: 0.23 (0.09), residues: 3793 sheet: -0.63 (0.20), residues: 645 loop : -0.62 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 73 HIS 0.005 0.001 HIS U 549 PHE 0.026 0.001 PHE I 107 TYR 0.023 0.001 TYR 4 211 ARG 0.012 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 638 time to evaluate : 4.526 Fit side-chains revert: symmetry clash REVERT: 1 155 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7548 (tm-30) REVERT: 1 216 LEU cc_start: 0.8814 (mt) cc_final: 0.8368 (tt) REVERT: 1 263 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7865 (tp) REVERT: 1 276 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8919 (pt) REVERT: 1 486 ASP cc_start: 0.7359 (m-30) cc_final: 0.7052 (m-30) REVERT: 2 74 ASN cc_start: 0.8304 (t0) cc_final: 0.7900 (m-40) REVERT: 2 131 LYS cc_start: 0.7671 (mppt) cc_final: 0.7243 (ptpt) REVERT: 2 154 ASP cc_start: 0.6746 (t0) cc_final: 0.5753 (p0) REVERT: 3 276 GLU cc_start: 0.8235 (tt0) cc_final: 0.7954 (tp30) REVERT: 4 54 GLU cc_start: 0.7962 (pt0) cc_final: 0.7737 (pt0) REVERT: 4 133 ASP cc_start: 0.8186 (t0) cc_final: 0.7916 (t0) REVERT: 5 59 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8538 (p0) REVERT: 5 115 ILE cc_start: 0.9042 (tp) cc_final: 0.8584 (tp) REVERT: 8 69 LYS cc_start: 0.8009 (mttt) cc_final: 0.6009 (tmtt) REVERT: 9 1 MET cc_start: 0.2106 (ptt) cc_final: -0.0604 (mpp) REVERT: 9 27 ASN cc_start: 0.7639 (t0) cc_final: 0.7308 (t160) REVERT: 9 33 LYS cc_start: 0.8559 (tttm) cc_final: 0.8213 (tptt) REVERT: 9 56 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8549 (p0) REVERT: 9 80 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7636 (mm110) REVERT: A 81 MET cc_start: 0.7998 (ttp) cc_final: 0.7758 (ttp) REVERT: A 102 TYR cc_start: 0.7815 (m-80) cc_final: 0.7599 (m-80) REVERT: B 81 MET cc_start: 0.8729 (ttp) cc_final: 0.8522 (ttp) REVERT: I 60 LYS cc_start: 0.8102 (mttm) cc_final: 0.7885 (ttmm) REVERT: J 119 LEU cc_start: 0.7871 (tt) cc_final: 0.6487 (mt) REVERT: M 168 MET cc_start: 0.8045 (mmt) cc_final: 0.7790 (mmt) REVERT: M 230 THR cc_start: 0.9175 (t) cc_final: 0.8848 (m) REVERT: M 294 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8658 (mp) REVERT: M 324 LYS cc_start: 0.6880 (tptt) cc_final: 0.6519 (tmtt) REVERT: P 49 THR cc_start: 0.7614 (OUTLIER) cc_final: 0.7410 (t) REVERT: P 66 GLN cc_start: 0.8392 (mt0) cc_final: 0.7904 (mt0) REVERT: P 127 ASP cc_start: 0.8359 (t70) cc_final: 0.7938 (t70) REVERT: P 136 GLU cc_start: 0.8011 (mp0) cc_final: 0.7288 (mp0) REVERT: P 157 ILE cc_start: 0.8931 (mt) cc_final: 0.8589 (mt) REVERT: P 186 MET cc_start: 0.4223 (mmm) cc_final: 0.3661 (mmm) REVERT: P 191 ASP cc_start: 0.7804 (t0) cc_final: 0.7174 (p0) REVERT: P 218 PHE cc_start: 0.8622 (t80) cc_final: 0.8301 (t80) REVERT: P 227 LEU cc_start: 0.8611 (mt) cc_final: 0.8383 (mt) REVERT: Q 10 ARG cc_start: 0.8252 (tpp-160) cc_final: 0.7627 (mmt180) REVERT: Q 52 TYR cc_start: 0.7084 (m-80) cc_final: 0.6448 (m-80) REVERT: S 62 MET cc_start: 0.7570 (mmm) cc_final: 0.7300 (mmm) REVERT: S 220 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7814 (mm) REVERT: S 240 SER cc_start: 0.8820 (m) cc_final: 0.8397 (p) REVERT: S 244 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7404 (ttp80) REVERT: T 49 ARG cc_start: 0.8368 (mtp-110) cc_final: 0.7880 (mtp85) REVERT: T 475 GLU cc_start: 0.6003 (tm-30) cc_final: 0.5434 (mm-30) REVERT: T 479 ARG cc_start: 0.6935 (mmp-170) cc_final: 0.5186 (tpt170) REVERT: U 72 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8081 (tm-30) REVERT: U 74 GLU cc_start: 0.8129 (pp20) cc_final: 0.7568 (pm20) REVERT: U 474 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.6911 (mp) REVERT: U 496 ARG cc_start: 0.8535 (mtt180) cc_final: 0.8293 (mtt-85) REVERT: U 539 ASN cc_start: 0.8193 (m-40) cc_final: 0.7719 (m110) REVERT: V 471 GLN cc_start: 0.6507 (tp40) cc_final: 0.6275 (tp40) REVERT: X 538 VAL cc_start: 0.6955 (OUTLIER) cc_final: 0.6616 (m) REVERT: Y 430 LYS cc_start: 0.6103 (ptmt) cc_final: 0.5877 (mtmm) REVERT: Z 82 ASP cc_start: 0.7711 (t0) cc_final: 0.7300 (t0) REVERT: Z 266 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8394 (tt) outliers start: 142 outliers final: 106 residues processed: 741 average time/residue: 0.5431 time to fit residues: 666.3928 Evaluate side-chains 725 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 609 time to evaluate : 4.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 36 THR Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 263 LEU Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 437 VAL Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 27 ASP Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 294 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 192 LYS Chi-restraints excluded: chain P residue 216 GLU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 474 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 210 ASP Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 208 SER Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 416 ILE Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 530 LEU Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 266 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 384 optimal weight: 0.9980 chunk 493 optimal weight: 4.9990 chunk 382 optimal weight: 3.9990 chunk 568 optimal weight: 2.9990 chunk 377 optimal weight: 1.9990 chunk 672 optimal weight: 1.9990 chunk 421 optimal weight: 0.0040 chunk 410 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 111 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 GLN 8 78 HIS E 98 GLN F 92 ASN F 98 GLN G 98 GLN P 66 GLN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN T 461 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 244 ASN Y 241 ASN Y 440 GLN Z 78 GLN ** Z 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 54694 Z= 0.213 Angle : 0.515 15.235 74172 Z= 0.261 Chirality : 0.042 0.249 8690 Planarity : 0.004 0.053 9512 Dihedral : 6.231 168.450 7675 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 2.75 % Allowed : 12.59 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.10), residues: 7039 helix: 0.31 (0.09), residues: 3818 sheet: -0.58 (0.20), residues: 645 loop : -0.61 (0.13), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 73 HIS 0.005 0.001 HIS V 83 PHE 0.026 0.001 PHE P 221 TYR 0.022 0.001 TYR 4 211 ARG 0.012 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 619 time to evaluate : 4.506 Fit side-chains revert: symmetry clash REVERT: 1 155 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7559 (tm-30) REVERT: 1 216 LEU cc_start: 0.8810 (mt) cc_final: 0.8365 (tt) REVERT: 1 219 LYS cc_start: 0.7943 (mttp) cc_final: 0.7727 (mmtm) REVERT: 1 276 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8936 (pt) REVERT: 1 399 MET cc_start: 0.8677 (mmt) cc_final: 0.8420 (mmt) REVERT: 1 441 PHE cc_start: 0.7574 (m-10) cc_final: 0.6954 (m-10) REVERT: 1 486 ASP cc_start: 0.7368 (m-30) cc_final: 0.7057 (m-30) REVERT: 2 74 ASN cc_start: 0.8292 (t0) cc_final: 0.7859 (m-40) REVERT: 2 131 LYS cc_start: 0.7710 (mppt) cc_final: 0.7249 (ptpt) REVERT: 2 154 ASP cc_start: 0.6737 (t0) cc_final: 0.5734 (p0) REVERT: 3 276 GLU cc_start: 0.8290 (tt0) cc_final: 0.7995 (tp30) REVERT: 4 54 GLU cc_start: 0.7990 (pt0) cc_final: 0.7757 (pt0) REVERT: 4 133 ASP cc_start: 0.8222 (t0) cc_final: 0.7949 (t0) REVERT: 7 60 GLN cc_start: 0.7227 (tt0) cc_final: 0.6964 (tt0) REVERT: 8 3 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8244 (tt) REVERT: 8 69 LYS cc_start: 0.8019 (mttt) cc_final: 0.6012 (tmtt) REVERT: 9 1 MET cc_start: 0.2058 (ptt) cc_final: -0.0584 (mpp) REVERT: 9 27 ASN cc_start: 0.7650 (t0) cc_final: 0.7328 (t0) REVERT: 9 33 LYS cc_start: 0.8559 (tttm) cc_final: 0.8210 (tptt) REVERT: 9 56 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8510 (p0) REVERT: 9 80 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7710 (mm110) REVERT: A 81 MET cc_start: 0.8000 (ttp) cc_final: 0.7761 (ttp) REVERT: A 102 TYR cc_start: 0.7823 (m-80) cc_final: 0.7600 (m-80) REVERT: B 81 MET cc_start: 0.8755 (ttp) cc_final: 0.8531 (ttp) REVERT: J 119 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.6474 (mt) REVERT: M 168 MET cc_start: 0.8054 (mmt) cc_final: 0.7802 (mmt) REVERT: M 230 THR cc_start: 0.9179 (t) cc_final: 0.8850 (m) REVERT: M 294 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8665 (mp) REVERT: M 324 LYS cc_start: 0.6867 (tptt) cc_final: 0.6515 (tmtt) REVERT: P 49 THR cc_start: 0.7628 (OUTLIER) cc_final: 0.7401 (t) REVERT: P 66 GLN cc_start: 0.8351 (mt0) cc_final: 0.7933 (mt0) REVERT: P 127 ASP cc_start: 0.8348 (t70) cc_final: 0.7927 (t70) REVERT: P 136 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: P 157 ILE cc_start: 0.8947 (mt) cc_final: 0.8633 (mt) REVERT: P 186 MET cc_start: 0.4016 (mmm) cc_final: 0.3691 (mmm) REVERT: P 191 ASP cc_start: 0.7808 (t0) cc_final: 0.7222 (p0) REVERT: P 192 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8354 (mtpt) REVERT: P 218 PHE cc_start: 0.8634 (t80) cc_final: 0.8305 (t80) REVERT: P 227 LEU cc_start: 0.8617 (mt) cc_final: 0.8394 (mt) REVERT: Q 10 ARG cc_start: 0.8247 (tpp-160) cc_final: 0.7772 (mmt180) REVERT: Q 52 TYR cc_start: 0.7225 (m-80) cc_final: 0.6552 (m-80) REVERT: S 48 ARG cc_start: 0.7085 (ttt-90) cc_final: 0.6828 (ttt-90) REVERT: S 62 MET cc_start: 0.7564 (mmm) cc_final: 0.7292 (mmm) REVERT: S 153 ILE cc_start: 0.7170 (tt) cc_final: 0.6727 (pt) REVERT: S 220 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7813 (mm) REVERT: S 240 SER cc_start: 0.8814 (m) cc_final: 0.8397 (p) REVERT: S 244 ARG cc_start: 0.7817 (ttm-80) cc_final: 0.7394 (ttp80) REVERT: T 49 ARG cc_start: 0.8386 (mtp-110) cc_final: 0.7801 (mtp85) REVERT: T 475 GLU cc_start: 0.6265 (tm-30) cc_final: 0.5712 (mm-30) REVERT: T 479 ARG cc_start: 0.6953 (mmp-170) cc_final: 0.5219 (tpt170) REVERT: U 72 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8062 (tm-30) REVERT: U 74 GLU cc_start: 0.8199 (pp20) cc_final: 0.7610 (pm20) REVERT: U 474 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6893 (mp) REVERT: U 496 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8321 (mtt-85) REVERT: U 539 ASN cc_start: 0.8275 (m-40) cc_final: 0.7809 (m110) REVERT: V 471 GLN cc_start: 0.6530 (tp40) cc_final: 0.6298 (tp40) REVERT: X 538 VAL cc_start: 0.6967 (OUTLIER) cc_final: 0.6623 (m) REVERT: Y 366 ARG cc_start: 0.7674 (ttm110) cc_final: 0.7377 (ttm110) REVERT: Y 430 LYS cc_start: 0.6109 (ptmt) cc_final: 0.5888 (mtmm) REVERT: Y 441 ARG cc_start: 0.8398 (mmt-90) cc_final: 0.8062 (tpp80) REVERT: Z 82 ASP cc_start: 0.7724 (t0) cc_final: 0.7313 (t0) REVERT: Z 266 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8427 (tt) outliers start: 155 outliers final: 117 residues processed: 728 average time/residue: 0.5380 time to fit residues: 649.4381 Evaluate side-chains 735 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 606 time to evaluate : 4.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 36 THR Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 437 VAL Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 154 LEU Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 27 ASP Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 294 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 192 LYS Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 474 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 210 ASP Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 512 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 208 SER Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 484 MET Chi-restraints excluded: chain Y residue 530 LEU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 280 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 0.0980 chunk 268 optimal weight: 0.3980 chunk 401 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 427 optimal weight: 4.9990 chunk 458 optimal weight: 1.9990 chunk 332 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 528 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 GLN 8 78 HIS F 98 GLN G 98 GLN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN T 461 GLN T 539 ASN U 134 ASN U 497 GLN Y 440 GLN ** Z 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 54694 Z= 0.177 Angle : 0.503 11.823 74172 Z= 0.255 Chirality : 0.041 0.259 8690 Planarity : 0.004 0.060 9512 Dihedral : 6.155 177.493 7675 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.55 % Favored : 96.33 % Rotamer: Outliers : 2.57 % Allowed : 13.09 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.10), residues: 7039 helix: 0.46 (0.09), residues: 3811 sheet: -0.51 (0.20), residues: 645 loop : -0.55 (0.13), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 73 HIS 0.005 0.001 HIS V 83 PHE 0.027 0.001 PHE I 107 TYR 0.022 0.001 TYR 4 211 ARG 0.012 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 641 time to evaluate : 4.463 Fit side-chains revert: symmetry clash REVERT: 1 155 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7553 (tm-30) REVERT: 1 216 LEU cc_start: 0.8803 (mt) cc_final: 0.8353 (tt) REVERT: 1 219 LYS cc_start: 0.7929 (mttp) cc_final: 0.7701 (mmtm) REVERT: 1 276 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8906 (pt) REVERT: 1 399 MET cc_start: 0.8674 (mmt) cc_final: 0.8417 (mmt) REVERT: 1 441 PHE cc_start: 0.7524 (m-10) cc_final: 0.6939 (m-10) REVERT: 1 486 ASP cc_start: 0.7361 (m-30) cc_final: 0.7054 (m-30) REVERT: 2 74 ASN cc_start: 0.8292 (t0) cc_final: 0.7862 (m-40) REVERT: 2 131 LYS cc_start: 0.7696 (mppt) cc_final: 0.7235 (ptpt) REVERT: 2 154 ASP cc_start: 0.6745 (t0) cc_final: 0.5749 (p0) REVERT: 2 246 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7554 (mt-10) REVERT: 3 276 GLU cc_start: 0.8286 (tt0) cc_final: 0.8003 (tp30) REVERT: 4 54 GLU cc_start: 0.7967 (pt0) cc_final: 0.7740 (pt0) REVERT: 4 133 ASP cc_start: 0.8256 (t0) cc_final: 0.7970 (t0) REVERT: 7 60 GLN cc_start: 0.7182 (tt0) cc_final: 0.6951 (tt0) REVERT: 8 69 LYS cc_start: 0.8002 (mttt) cc_final: 0.6006 (tmtt) REVERT: 9 1 MET cc_start: 0.1924 (ptt) cc_final: -0.0544 (mpp) REVERT: 9 27 ASN cc_start: 0.7645 (t0) cc_final: 0.7325 (t0) REVERT: 9 33 LYS cc_start: 0.8542 (tttm) cc_final: 0.8207 (tptt) REVERT: 9 56 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8516 (p0) REVERT: 9 80 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7683 (mm110) REVERT: A 81 MET cc_start: 0.7986 (ttp) cc_final: 0.7750 (ttp) REVERT: A 102 TYR cc_start: 0.7839 (m-80) cc_final: 0.7537 (m-80) REVERT: B 81 MET cc_start: 0.8746 (ttp) cc_final: 0.8534 (ttp) REVERT: I 60 LYS cc_start: 0.8083 (mttm) cc_final: 0.7711 (ttmm) REVERT: J 119 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.6462 (mt) REVERT: M 168 MET cc_start: 0.8046 (mmt) cc_final: 0.7798 (mmt) REVERT: M 230 THR cc_start: 0.9147 (t) cc_final: 0.8837 (m) REVERT: M 324 LYS cc_start: 0.6861 (tptt) cc_final: 0.6517 (tmtt) REVERT: P 66 GLN cc_start: 0.8272 (mt0) cc_final: 0.7972 (mt0) REVERT: P 127 ASP cc_start: 0.8329 (t70) cc_final: 0.7902 (t70) REVERT: P 136 GLU cc_start: 0.8019 (mp0) cc_final: 0.7307 (mp0) REVERT: P 157 ILE cc_start: 0.8954 (mt) cc_final: 0.8615 (mt) REVERT: P 191 ASP cc_start: 0.7786 (t0) cc_final: 0.7220 (p0) REVERT: P 192 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8327 (mtpt) REVERT: P 227 LEU cc_start: 0.8614 (mt) cc_final: 0.8394 (mt) REVERT: Q 10 ARG cc_start: 0.8250 (tpp-160) cc_final: 0.7763 (mmt180) REVERT: Q 52 TYR cc_start: 0.7210 (m-80) cc_final: 0.6567 (m-80) REVERT: S 48 ARG cc_start: 0.7075 (ttt-90) cc_final: 0.6828 (ttt-90) REVERT: S 62 MET cc_start: 0.7550 (mmm) cc_final: 0.7280 (mmm) REVERT: S 153 ILE cc_start: 0.6996 (tt) cc_final: 0.6551 (pt) REVERT: S 220 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7813 (mm) REVERT: S 240 SER cc_start: 0.8806 (m) cc_final: 0.8385 (p) REVERT: S 244 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7386 (ttp80) REVERT: T 49 ARG cc_start: 0.8373 (mtp-110) cc_final: 0.7791 (mtp85) REVERT: T 475 GLU cc_start: 0.6235 (tm-30) cc_final: 0.5691 (mm-30) REVERT: T 479 ARG cc_start: 0.6968 (mmp-170) cc_final: 0.5189 (tpt170) REVERT: U 72 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8092 (tm-30) REVERT: U 74 GLU cc_start: 0.8217 (pp20) cc_final: 0.7588 (pm20) REVERT: U 474 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6870 (mp) REVERT: U 496 ARG cc_start: 0.8533 (mtt180) cc_final: 0.8304 (mtt-85) REVERT: V 287 MET cc_start: 0.8251 (tpt) cc_final: 0.7890 (tpt) REVERT: V 471 GLN cc_start: 0.6506 (tp40) cc_final: 0.6286 (tp40) REVERT: X 538 VAL cc_start: 0.6932 (OUTLIER) cc_final: 0.6598 (m) REVERT: Y 366 ARG cc_start: 0.7660 (ttm110) cc_final: 0.7371 (ttm110) REVERT: Y 430 LYS cc_start: 0.6093 (ptmt) cc_final: 0.5876 (mtmm) REVERT: Y 441 ARG cc_start: 0.8369 (mmt-90) cc_final: 0.7969 (mpt180) REVERT: Z 82 ASP cc_start: 0.7710 (t0) cc_final: 0.7304 (t0) REVERT: Z 266 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8395 (tt) REVERT: Z 422 MET cc_start: 0.7973 (mmm) cc_final: 0.7571 (mmm) outliers start: 145 outliers final: 119 residues processed: 743 average time/residue: 0.5519 time to fit residues: 676.5175 Evaluate side-chains 741 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 614 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 36 THR Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 154 LEU Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 27 ASP Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 192 LYS Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 474 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 445 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 210 ASP Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 512 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 416 ILE Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 530 LEU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 440 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 1.9990 chunk 644 optimal weight: 0.8980 chunk 588 optimal weight: 0.2980 chunk 626 optimal weight: 0.9990 chunk 377 optimal weight: 0.9990 chunk 273 optimal weight: 7.9990 chunk 492 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 chunk 566 optimal weight: 2.9990 chunk 592 optimal weight: 3.9990 chunk 624 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 GLN 8 78 HIS B 98 GLN F 98 GLN G 98 GLN P 71 GLN Q 49 GLN R 181 ASN T 461 GLN T 539 ASN U 134 ASN U 539 ASN Y 440 GLN Z 78 GLN ** Z 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 54694 Z= 0.196 Angle : 0.517 19.019 74172 Z= 0.261 Chirality : 0.041 0.279 8690 Planarity : 0.004 0.060 9512 Dihedral : 6.088 170.719 7675 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.76 % Favored : 96.12 % Rotamer: Outliers : 2.52 % Allowed : 13.49 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.10), residues: 7039 helix: 0.54 (0.09), residues: 3802 sheet: -0.47 (0.20), residues: 646 loop : -0.48 (0.13), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 73 HIS 0.005 0.001 HIS V 83 PHE 0.027 0.001 PHE I 107 TYR 0.022 0.001 TYR 4 211 ARG 0.013 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 623 time to evaluate : 4.893 Fit side-chains revert: symmetry clash REVERT: 1 136 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: 1 155 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7548 (tm-30) REVERT: 1 216 LEU cc_start: 0.8788 (mt) cc_final: 0.8355 (tt) REVERT: 1 276 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8897 (pt) REVERT: 1 399 MET cc_start: 0.8670 (mmt) cc_final: 0.8411 (mmt) REVERT: 1 441 PHE cc_start: 0.7550 (m-10) cc_final: 0.7102 (m-10) REVERT: 1 486 ASP cc_start: 0.7359 (m-30) cc_final: 0.7054 (m-30) REVERT: 2 74 ASN cc_start: 0.8301 (t0) cc_final: 0.7804 (m-40) REVERT: 2 131 LYS cc_start: 0.7725 (mppt) cc_final: 0.7239 (ptpt) REVERT: 2 154 ASP cc_start: 0.6736 (t0) cc_final: 0.5803 (p0) REVERT: 3 276 GLU cc_start: 0.8297 (tt0) cc_final: 0.8017 (tp30) REVERT: 4 54 GLU cc_start: 0.7973 (pt0) cc_final: 0.7749 (pt0) REVERT: 4 133 ASP cc_start: 0.8260 (t0) cc_final: 0.7976 (t0) REVERT: 7 60 GLN cc_start: 0.7175 (tt0) cc_final: 0.6974 (tt0) REVERT: 8 69 LYS cc_start: 0.7992 (mttt) cc_final: 0.5994 (tmtt) REVERT: 9 1 MET cc_start: 0.1861 (ptt) cc_final: -0.0521 (mpp) REVERT: 9 27 ASN cc_start: 0.7675 (t0) cc_final: 0.7349 (t0) REVERT: 9 33 LYS cc_start: 0.8542 (tttm) cc_final: 0.8207 (tptt) REVERT: 9 56 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8490 (p0) REVERT: A 81 MET cc_start: 0.8007 (ttp) cc_final: 0.7767 (ttp) REVERT: B 81 MET cc_start: 0.8765 (ttp) cc_final: 0.8544 (ttp) REVERT: I 60 LYS cc_start: 0.8035 (mttm) cc_final: 0.7696 (ttmm) REVERT: J 119 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.6374 (mt) REVERT: M 168 MET cc_start: 0.8049 (mmt) cc_final: 0.7799 (mmt) REVERT: M 230 THR cc_start: 0.9148 (t) cc_final: 0.8843 (m) REVERT: M 270 MET cc_start: 0.6290 (tmm) cc_final: 0.5449 (mmt) REVERT: M 324 LYS cc_start: 0.6876 (tptt) cc_final: 0.6520 (tmtt) REVERT: P 66 GLN cc_start: 0.8195 (mt0) cc_final: 0.7884 (mt0) REVERT: P 127 ASP cc_start: 0.8274 (t70) cc_final: 0.7896 (t70) REVERT: P 136 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: P 157 ILE cc_start: 0.8974 (mt) cc_final: 0.8635 (mt) REVERT: P 191 ASP cc_start: 0.7793 (t0) cc_final: 0.7209 (p0) REVERT: P 192 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8403 (mtpt) REVERT: P 227 LEU cc_start: 0.8619 (mt) cc_final: 0.8400 (mt) REVERT: Q 10 ARG cc_start: 0.8259 (tpp-160) cc_final: 0.7756 (mmt180) REVERT: Q 52 TYR cc_start: 0.7215 (m-80) cc_final: 0.6568 (m-80) REVERT: S 48 ARG cc_start: 0.7033 (ttt-90) cc_final: 0.6796 (ttt-90) REVERT: S 62 MET cc_start: 0.7557 (mmm) cc_final: 0.7279 (mmm) REVERT: S 153 ILE cc_start: 0.6999 (tt) cc_final: 0.6509 (pt) REVERT: S 220 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7818 (mm) REVERT: S 240 SER cc_start: 0.8799 (m) cc_final: 0.8381 (p) REVERT: S 244 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7391 (ttp80) REVERT: T 49 ARG cc_start: 0.8379 (mtp-110) cc_final: 0.7796 (mtp85) REVERT: T 475 GLU cc_start: 0.6258 (tm-30) cc_final: 0.5692 (mm-30) REVERT: T 479 ARG cc_start: 0.6976 (mmp-170) cc_final: 0.5219 (tpt170) REVERT: U 72 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8092 (tm-30) REVERT: U 74 GLU cc_start: 0.8252 (pp20) cc_final: 0.7703 (pm20) REVERT: U 474 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6825 (mp) REVERT: U 496 ARG cc_start: 0.8498 (mtt180) cc_final: 0.8266 (mtt-85) REVERT: U 535 ILE cc_start: 0.8068 (tp) cc_final: 0.7854 (tp) REVERT: X 538 VAL cc_start: 0.6934 (OUTLIER) cc_final: 0.6598 (m) REVERT: Y 366 ARG cc_start: 0.7642 (ttm110) cc_final: 0.7365 (ttm110) REVERT: Y 430 LYS cc_start: 0.6092 (ptmt) cc_final: 0.5847 (mtmm) REVERT: Y 441 ARG cc_start: 0.8349 (mmt-90) cc_final: 0.7961 (mpt180) REVERT: Z 82 ASP cc_start: 0.7718 (t0) cc_final: 0.7310 (t0) REVERT: Z 266 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8416 (tt) outliers start: 142 outliers final: 124 residues processed: 721 average time/residue: 0.5524 time to fit residues: 658.8143 Evaluate side-chains 746 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 612 time to evaluate : 4.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 36 THR Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 136 GLU Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 437 VAL Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 154 LEU Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 27 ASP Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 192 LYS Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 474 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 445 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 210 ASP Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 512 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 208 SER Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 484 MET Chi-restraints excluded: chain Y residue 530 LEU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 440 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 0.9980 chunk 662 optimal weight: 2.9990 chunk 404 optimal weight: 0.6980 chunk 314 optimal weight: 10.0000 chunk 460 optimal weight: 0.7980 chunk 695 optimal weight: 4.9990 chunk 640 optimal weight: 0.4980 chunk 553 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 427 optimal weight: 3.9990 chunk 339 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 44 ASN ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 GLN 8 78 HIS F 98 GLN G 98 GLN P 59 GLN R 181 ASN T 461 GLN T 539 ASN U 134 ASN Y 440 GLN ** Z 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 54694 Z= 0.215 Angle : 0.523 17.795 74172 Z= 0.265 Chirality : 0.042 0.292 8690 Planarity : 0.004 0.061 9512 Dihedral : 6.047 158.992 7675 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.84 % Favored : 96.05 % Rotamer: Outliers : 2.47 % Allowed : 13.58 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.10), residues: 7039 helix: 0.53 (0.09), residues: 3824 sheet: -0.44 (0.20), residues: 645 loop : -0.52 (0.13), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 73 HIS 0.005 0.001 HIS V 83 PHE 0.027 0.001 PHE I 107 TYR 0.022 0.001 TYR 4 211 ARG 0.014 0.000 ARG V 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 608 time to evaluate : 4.517 Fit side-chains revert: symmetry clash REVERT: 1 136 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: 1 155 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7538 (tm-30) REVERT: 1 216 LEU cc_start: 0.8806 (mt) cc_final: 0.8373 (tt) REVERT: 1 276 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8909 (pt) REVERT: 1 399 MET cc_start: 0.8671 (mmt) cc_final: 0.8416 (mmt) REVERT: 1 441 PHE cc_start: 0.7661 (m-10) cc_final: 0.7344 (m-10) REVERT: 1 486 ASP cc_start: 0.7364 (m-30) cc_final: 0.7058 (m-30) REVERT: 2 74 ASN cc_start: 0.8313 (t0) cc_final: 0.7799 (m-40) REVERT: 2 131 LYS cc_start: 0.7699 (mppt) cc_final: 0.7221 (ptpt) REVERT: 2 154 ASP cc_start: 0.6743 (t0) cc_final: 0.5807 (p0) REVERT: 3 276 GLU cc_start: 0.8313 (tt0) cc_final: 0.8061 (tp30) REVERT: 4 54 GLU cc_start: 0.7987 (pt0) cc_final: 0.7760 (pt0) REVERT: 4 133 ASP cc_start: 0.8268 (t0) cc_final: 0.7988 (t0) REVERT: 7 60 GLN cc_start: 0.7162 (tt0) cc_final: 0.6962 (tt0) REVERT: 8 3 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8232 (tt) REVERT: 8 69 LYS cc_start: 0.8005 (mttt) cc_final: 0.6008 (tmtt) REVERT: 9 1 MET cc_start: 0.1852 (ptt) cc_final: -0.0526 (mpp) REVERT: 9 33 LYS cc_start: 0.8536 (tttm) cc_final: 0.8195 (tptt) REVERT: 9 56 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8497 (p0) REVERT: A 81 MET cc_start: 0.8027 (ttp) cc_final: 0.7787 (ttp) REVERT: B 81 MET cc_start: 0.8771 (ttp) cc_final: 0.8550 (ttp) REVERT: J 119 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.6382 (mt) REVERT: M 168 MET cc_start: 0.8057 (mmt) cc_final: 0.7815 (mmt) REVERT: M 230 THR cc_start: 0.9153 (t) cc_final: 0.8848 (m) REVERT: M 270 MET cc_start: 0.6372 (tmm) cc_final: 0.5512 (mmt) REVERT: M 324 LYS cc_start: 0.6887 (tptt) cc_final: 0.6521 (tmtt) REVERT: P 66 GLN cc_start: 0.8211 (mt0) cc_final: 0.7937 (mt0) REVERT: P 127 ASP cc_start: 0.8278 (t70) cc_final: 0.7893 (t70) REVERT: P 136 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: P 191 ASP cc_start: 0.7787 (t0) cc_final: 0.7082 (p0) REVERT: P 192 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8366 (mtpt) REVERT: P 227 LEU cc_start: 0.8628 (mt) cc_final: 0.8402 (mt) REVERT: Q 10 ARG cc_start: 0.8263 (tpp-160) cc_final: 0.7751 (mmt180) REVERT: Q 52 TYR cc_start: 0.7193 (m-80) cc_final: 0.6532 (m-80) REVERT: S 62 MET cc_start: 0.7550 (mmm) cc_final: 0.7247 (mmm) REVERT: S 153 ILE cc_start: 0.7020 (tt) cc_final: 0.6522 (pt) REVERT: S 220 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7818 (mm) REVERT: S 244 ARG cc_start: 0.7823 (ttm-80) cc_final: 0.7389 (ttp80) REVERT: T 49 ARG cc_start: 0.8386 (mtp-110) cc_final: 0.7803 (mtp85) REVERT: T 475 GLU cc_start: 0.6269 (tm-30) cc_final: 0.5706 (mm-30) REVERT: T 479 ARG cc_start: 0.6984 (mmp-170) cc_final: 0.5223 (tpt170) REVERT: U 72 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8095 (tm-30) REVERT: U 74 GLU cc_start: 0.8238 (pp20) cc_final: 0.7702 (pm20) REVERT: U 474 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6810 (mp) REVERT: V 287 MET cc_start: 0.8302 (tpt) cc_final: 0.7943 (tpt) REVERT: X 538 VAL cc_start: 0.6929 (OUTLIER) cc_final: 0.6593 (m) REVERT: Y 366 ARG cc_start: 0.7624 (ttm110) cc_final: 0.7346 (ttm110) REVERT: Y 430 LYS cc_start: 0.6101 (ptmt) cc_final: 0.5883 (mtmm) REVERT: Y 441 ARG cc_start: 0.8356 (mmt-90) cc_final: 0.7965 (mpt180) REVERT: Z 82 ASP cc_start: 0.7726 (t0) cc_final: 0.7317 (t0) REVERT: Z 266 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8441 (tt) outliers start: 139 outliers final: 121 residues processed: 704 average time/residue: 0.5606 time to fit residues: 653.4306 Evaluate side-chains 730 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 598 time to evaluate : 4.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 36 THR Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 136 GLU Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 154 LEU Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 27 ASP Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 192 LYS Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 474 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 445 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 512 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 208 SER Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 484 MET Chi-restraints excluded: chain Y residue 530 LEU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 440 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 3.9990 chunk 589 optimal weight: 10.0000 chunk 169 optimal weight: 0.0070 chunk 510 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 554 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 569 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 150 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 GLN 8 78 HIS 9 27 ASN F 98 GLN G 98 GLN P 59 GLN R 104 HIS R 181 ASN T 461 GLN T 539 ASN U 61 HIS U 134 ASN Y 440 GLN Z 388 ASN Z 440 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.128620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.099487 restraints weight = 75779.642| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.68 r_work: 0.2941 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 54694 Z= 0.240 Angle : 0.536 16.539 74172 Z= 0.271 Chirality : 0.042 0.296 8690 Planarity : 0.004 0.062 9512 Dihedral : 6.038 145.068 7675 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.94 % Favored : 95.95 % Rotamer: Outliers : 2.40 % Allowed : 13.73 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.10), residues: 7039 helix: 0.52 (0.09), residues: 3833 sheet: -0.42 (0.20), residues: 640 loop : -0.49 (0.13), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 73 HIS 0.005 0.001 HIS V 83 PHE 0.027 0.001 PHE I 107 TYR 0.025 0.001 TYR X 248 ARG 0.014 0.000 ARG V 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12447.36 seconds wall clock time: 219 minutes 40.05 seconds (13180.05 seconds total)