Starting phenix.real_space_refine on Sat Mar 23 23:03:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ray_4787/03_2024/6ray_4787_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ray_4787/03_2024/6ray_4787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ray_4787/03_2024/6ray_4787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ray_4787/03_2024/6ray_4787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ray_4787/03_2024/6ray_4787_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ray_4787/03_2024/6ray_4787_updated.pdb" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 29 5.49 5 S 208 5.16 5 C 24484 2.51 5 N 6871 2.21 5 O 7479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 43": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 ARG 58": "NH1" <-> "NH2" Residue "3 ARG 75": "NH1" <-> "NH2" Residue "3 ASP 94": "OD1" <-> "OD2" Residue "3 ARG 106": "NH1" <-> "NH2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 158": "OD1" <-> "OD2" Residue "3 ASP 177": "OD1" <-> "OD2" Residue "3 GLU 203": "OE1" <-> "OE2" Residue "3 ASP 224": "OD1" <-> "OD2" Residue "3 ARG 225": "NH1" <-> "NH2" Residue "3 ARG 231": "NH1" <-> "NH2" Residue "3 ARG 239": "NH1" <-> "NH2" Residue "3 ARG 245": "NH1" <-> "NH2" Residue "3 ARG 254": "NH1" <-> "NH2" Residue "3 GLU 268": "OE1" <-> "OE2" Residue "3 ARG 275": "NH1" <-> "NH2" Residue "3 GLU 292": "OE1" <-> "OE2" Residue "3 ARG 329": "NH1" <-> "NH2" Residue "3 ASP 333": "OD1" <-> "OD2" Residue "3 ARG 351": "NH1" <-> "NH2" Residue "3 TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 359": "NH1" <-> "NH2" Residue "3 ARG 366": "NH1" <-> "NH2" Residue "3 ARG 387": "NH1" <-> "NH2" Residue "3 ARG 414": "NH1" <-> "NH2" Residue "3 GLU 422": "OE1" <-> "OE2" Residue "3 ARG 425": "NH1" <-> "NH2" Residue "3 TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 453": "NH1" <-> "NH2" Residue "3 ASP 455": "OD1" <-> "OD2" Residue "3 ASP 475": "OD1" <-> "OD2" Residue "3 ASP 494": "OD1" <-> "OD2" Residue "3 ARG 501": "NH1" <-> "NH2" Residue "3 ARG 503": "NH1" <-> "NH2" Residue "3 ARG 550": "NH1" <-> "NH2" Residue "3 ARG 552": "NH1" <-> "NH2" Residue "3 ARG 563": "NH1" <-> "NH2" Residue "3 GLU 587": "OE1" <-> "OE2" Residue "3 ARG 590": "NH1" <-> "NH2" Residue "3 ARG 603": "NH1" <-> "NH2" Residue "3 ARG 610": "NH1" <-> "NH2" Residue "3 ARG 624": "NH1" <-> "NH2" Residue "3 GLU 641": "OE1" <-> "OE2" Residue "4 ARG 174": "NH1" <-> "NH2" Residue "4 ASP 190": "OD1" <-> "OD2" Residue "4 GLU 208": "OE1" <-> "OE2" Residue "4 ASP 224": "OD1" <-> "OD2" Residue "4 ARG 227": "NH1" <-> "NH2" Residue "4 ARG 251": "NH1" <-> "NH2" Residue "4 TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 283": "OD1" <-> "OD2" Residue "4 ARG 303": "NH1" <-> "NH2" Residue "4 ARG 324": "NH1" <-> "NH2" Residue "4 ARG 341": "NH1" <-> "NH2" Residue "4 ARG 346": "NH1" <-> "NH2" Residue "4 GLU 348": "OE1" <-> "OE2" Residue "4 ASP 380": "OD1" <-> "OD2" Residue "4 ASP 389": "OD1" <-> "OD2" Residue "4 ARG 390": "NH1" <-> "NH2" Residue "4 TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 425": "NH1" <-> "NH2" Residue "4 ASP 428": "OD1" <-> "OD2" Residue "4 GLU 436": "OE1" <-> "OE2" Residue "4 ARG 447": "NH1" <-> "NH2" Residue "4 ARG 463": "NH1" <-> "NH2" Residue "4 ARG 499": "NH1" <-> "NH2" Residue "4 ARG 503": "NH1" <-> "NH2" Residue "4 ARG 531": "NH1" <-> "NH2" Residue "4 TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 554": "OE1" <-> "OE2" Residue "4 GLU 577": "OE1" <-> "OE2" Residue "4 ASP 583": "OD1" <-> "OD2" Residue "4 GLU 623": "OE1" <-> "OE2" Residue "4 ARG 629": "NH1" <-> "NH2" Residue "4 VAL 652": "CG1" <-> "CG2" Residue "4 GLU 658": "OE1" <-> "OE2" Residue "4 ARG 663": "NH1" <-> "NH2" Residue "4 TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 676": "NH1" <-> "NH2" Residue "4 ASP 681": "OD1" <-> "OD2" Residue "4 ARG 690": "NH1" <-> "NH2" Residue "4 ARG 697": "NH1" <-> "NH2" Residue "4 ARG 711": "NH1" <-> "NH2" Residue "4 ASP 718": "OD1" <-> "OD2" Residue "4 ARG 726": "NH1" <-> "NH2" Residue "4 ARG 734": "NH1" <-> "NH2" Residue "4 GLU 737": "OE1" <-> "OE2" Residue "4 ARG 750": "NH1" <-> "NH2" Residue "4 ARG 765": "NH1" <-> "NH2" Residue "7 ARG 3": "NH1" <-> "NH2" Residue "7 ARG 4": "NH1" <-> "NH2" Residue "7 ARG 10": "NH1" <-> "NH2" Residue "7 ASP 26": "OD1" <-> "OD2" Residue "7 ASP 53": "OD1" <-> "OD2" Residue "7 ARG 71": "NH1" <-> "NH2" Residue "7 ASP 121": "OD1" <-> "OD2" Residue "7 ARG 123": "NH1" <-> "NH2" Residue "7 ARG 133": "NH1" <-> "NH2" Residue "7 ASP 205": "OD1" <-> "OD2" Residue "7 ARG 212": "NH1" <-> "NH2" Residue "7 ARG 219": "NH1" <-> "NH2" Residue "7 TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 234": "OE1" <-> "OE2" Residue "7 ARG 258": "NH1" <-> "NH2" Residue "7 PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 302": "NH1" <-> "NH2" Residue "7 ASP 310": "OD1" <-> "OD2" Residue "7 ASP 330": "OD1" <-> "OD2" Residue "7 GLU 343": "OE1" <-> "OE2" Residue "7 ASP 349": "OD1" <-> "OD2" Residue "7 ARG 365": "NH1" <-> "NH2" Residue "7 ARG 372": "NH1" <-> "NH2" Residue "7 ASP 382": "OD1" <-> "OD2" Residue "7 ARG 396": "NH1" <-> "NH2" Residue "7 ARG 407": "NH1" <-> "NH2" Residue "7 ARG 455": "NH1" <-> "NH2" Residue "7 PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 494": "NH1" <-> "NH2" Residue "7 ARG 498": "NH1" <-> "NH2" Residue "7 ARG 499": "NH1" <-> "NH2" Residue "7 ARG 527": "NH1" <-> "NH2" Residue "7 ARG 532": "NH1" <-> "NH2" Residue "7 ARG 550": "NH1" <-> "NH2" Residue "7 ARG 561": "NH1" <-> "NH2" Residue "7 TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 568": "NH1" <-> "NH2" Residue "7 ARG 590": "NH1" <-> "NH2" Residue "7 ARG 593": "NH1" <-> "NH2" Residue "7 ARG 620": "NH1" <-> "NH2" Residue "7 ARG 635": "NH1" <-> "NH2" Residue "6 ARG 20": "NH1" <-> "NH2" Residue "6 ARG 42": "NH1" <-> "NH2" Residue "6 ARG 52": "NH1" <-> "NH2" Residue "6 PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 95": "NH1" <-> "NH2" Residue "6 ARG 114": "NH1" <-> "NH2" Residue "6 ARG 118": "NH1" <-> "NH2" Residue "6 ARG 160": "NH1" <-> "NH2" Residue "6 PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 175": "NH1" <-> "NH2" Residue "6 ARG 182": "NH1" <-> "NH2" Residue "6 PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 201": "NH1" <-> "NH2" Residue "6 GLU 208": "OE1" <-> "OE2" Residue "6 ARG 211": "NH1" <-> "NH2" Residue "6 ARG 216": "NH1" <-> "NH2" Residue "6 GLU 219": "OE1" <-> "OE2" Residue "6 ARG 223": "NH1" <-> "NH2" Residue "6 ARG 257": "NH1" <-> "NH2" Residue "6 ARG 263": "NH1" <-> "NH2" Residue "6 ARG 282": "NH1" <-> "NH2" Residue "6 ARG 287": "NH1" <-> "NH2" Residue "6 ARG 301": "NH1" <-> "NH2" Residue "6 ASP 316": "OD1" <-> "OD2" Residue "6 ARG 336": "NH1" <-> "NH2" Residue "6 ARG 358": "NH1" <-> "NH2" Residue "6 ARG 379": "NH1" <-> "NH2" Residue "6 PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 407": "NH1" <-> "NH2" Residue "6 ARG 427": "NH1" <-> "NH2" Residue "6 GLU 430": "OE1" <-> "OE2" Residue "6 ASP 433": "OD1" <-> "OD2" Residue "6 GLU 437": "OE1" <-> "OE2" Residue "6 ARG 460": "NH1" <-> "NH2" Residue "6 ASP 503": "OD1" <-> "OD2" Residue "6 ARG 504": "NH1" <-> "NH2" Residue "6 ARG 521": "NH1" <-> "NH2" Residue "6 ASP 523": "OD1" <-> "OD2" Residue "6 ASP 530": "OD1" <-> "OD2" Residue "6 ARG 542": "NH1" <-> "NH2" Residue "6 ASP 546": "OD1" <-> "OD2" Residue "6 GLU 556": "OE1" <-> "OE2" Residue "6 ARG 557": "NH1" <-> "NH2" Residue "6 ARG 561": "NH1" <-> "NH2" Residue "6 ARG 594": "NH1" <-> "NH2" Residue "6 ARG 596": "NH1" <-> "NH2" Residue "6 ARG 603": "NH1" <-> "NH2" Residue "6 ARG 631": "NH1" <-> "NH2" Residue "6 ARG 635": "NH1" <-> "NH2" Residue "6 ARG 642": "NH1" <-> "NH2" Residue "5 ARG 39": "NH1" <-> "NH2" Residue "5 PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 62": "NH1" <-> "NH2" Residue "5 GLU 68": "OE1" <-> "OE2" Residue "5 ASP 71": "OD1" <-> "OD2" Residue "5 GLU 77": "OE1" <-> "OE2" Residue "5 ARG 99": "NH1" <-> "NH2" Residue "5 GLU 113": "OE1" <-> "OE2" Residue "5 ARG 162": "NH1" <-> "NH2" Residue "5 ARG 199": "NH1" <-> "NH2" Residue "5 GLU 235": "OE1" <-> "OE2" Residue "5 ASP 245": "OD1" <-> "OD2" Residue "5 ARG 251": "NH1" <-> "NH2" Residue "5 ARG 267": "NH1" <-> "NH2" Residue "5 GLU 279": "OE1" <-> "OE2" Residue "5 TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 291": "NH1" <-> "NH2" Residue "5 ARG 307": "NH1" <-> "NH2" Residue "5 ASP 314": "OD1" <-> "OD2" Residue "5 ARG 320": "NH1" <-> "NH2" Residue "5 ARG 321": "NH1" <-> "NH2" Residue "5 GLU 330": "OE1" <-> "OE2" Residue "5 ARG 331": "NH1" <-> "NH2" Residue "5 ARG 344": "NH1" <-> "NH2" Residue "5 ARG 359": "NH1" <-> "NH2" Residue "5 ARG 361": "NH1" <-> "NH2" Residue "5 ARG 368": "NH1" <-> "NH2" Residue "5 ASP 379": "OD1" <-> "OD2" Residue "5 TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 422": "NH1" <-> "NH2" Residue "5 GLU 427": "OE1" <-> "OE2" Residue "5 ASP 435": "OD1" <-> "OD2" Residue "5 GLU 443": "OE1" <-> "OE2" Residue "5 ASP 493": "OD1" <-> "OD2" Residue "5 GLU 499": "OE1" <-> "OE2" Residue "5 ASP 522": "OD1" <-> "OD2" Residue "5 GLU 523": "OE1" <-> "OE2" Residue "5 GLU 552": "OE1" <-> "OE2" Residue "5 GLU 575": "OE1" <-> "OE2" Residue "5 ARG 610": "NH1" <-> "NH2" Residue "5 ARG 626": "NH1" <-> "NH2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ASP 149": "OD1" <-> "OD2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A ASP 525": "OD1" <-> "OD2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 565": "NH1" <-> "NH2" Residue "H TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 170": "OD1" <-> "OD2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "L GLU 64": "OE1" <-> "OE2" Residue "L ASP 67": "OD1" <-> "OD2" Residue "L ASP 69": "OD1" <-> "OD2" Residue "L GLU 72": "OE1" <-> "OE2" Residue "L GLU 111": "OE1" <-> "OE2" Residue "L PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 146": "OD1" <-> "OD2" Residue "L GLU 152": "OE1" <-> "OE2" Residue "L ASP 180": "OD1" <-> "OD2" Residue "M GLU 93": "OE1" <-> "OE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 139": "OD1" <-> "OD2" Residue "M GLU 158": "OE1" <-> "OE2" Residue "N GLU 23": "OE1" <-> "OE2" Residue "N ASP 27": "OD1" <-> "OD2" Residue "N ASP 28": "OD1" <-> "OD2" Residue "N GLU 40": "OE1" <-> "OE2" Residue "N TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 197": "OD1" <-> "OD2" Residue "2 ARG 177": "NH1" <-> "NH2" Residue "2 ARG 183": "NH1" <-> "NH2" Residue "2 ARG 189": "NH1" <-> "NH2" Residue "2 ARG 195": "NH1" <-> "NH2" Residue "2 ARG 201": "NH1" <-> "NH2" Residue "2 ARG 206": "NH1" <-> "NH2" Residue "2 GLU 277": "OE1" <-> "OE2" Residue "2 ARG 292": "NH1" <-> "NH2" Residue "2 GLU 331": "OE1" <-> "OE2" Residue "2 ARG 356": "NH1" <-> "NH2" Residue "2 GLU 365": "OE1" <-> "OE2" Residue "2 ARG 369": "NH1" <-> "NH2" Residue "2 ASP 380": "OD1" <-> "OD2" Residue "2 GLU 396": "OE1" <-> "OE2" Residue "2 ASP 408": "OD1" <-> "OD2" Residue "2 ASP 414": "OD1" <-> "OD2" Residue "2 ASP 443": "OD1" <-> "OD2" Residue "2 ASP 455": "OD1" <-> "OD2" Residue "2 ARG 457": "NH1" <-> "NH2" Residue "2 ARG 461": "NH1" <-> "NH2" Residue "2 ARG 478": "NH1" <-> "NH2" Residue "2 ARG 499": "NH1" <-> "NH2" Residue "2 ASP 575": "OD1" <-> "OD2" Residue "2 ASP 579": "OD1" <-> "OD2" Residue "2 ARG 621": "NH1" <-> "NH2" Residue "2 GLU 636": "OE1" <-> "OE2" Residue "2 ASP 657": "OD1" <-> "OD2" Residue "2 ARG 698": "NH1" <-> "NH2" Residue "2 TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 709": "NH1" <-> "NH2" Residue "2 ASP 718": "OD1" <-> "OD2" Residue "2 ARG 728": "NH1" <-> "NH2" Residue "2 ARG 742": "NH1" <-> "NH2" Residue "2 ARG 756": "NH1" <-> "NH2" Residue "2 ARG 760": "NH1" <-> "NH2" Residue "2 ARG 773": "NH1" <-> "NH2" Residue "2 GLU 777": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39071 Number of models: 1 Model: "" Number of chains: 18 Chain: "3" Number of atoms: 4685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4685 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 577} Chain breaks: 8 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "4" Number of atoms: 4901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4901 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 25, 'TRANS': 591} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "7" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4577 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 24, 'TRANS': 562} Unresolved chain links: 1 Chain breaks: 11 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "6" Number of atoms: 4748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4748 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 580} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "5" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4505 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 25, 'TRANS': 551} Chain breaks: 10 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 4555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4555 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 552} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1504 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1422 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1377 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1627 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 2, 'ILE%COO:oxt': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "2" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4731 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 571} Chain breaks: 5 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "X" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.34, per 1000 atoms: 0.49 Number of scatterers: 39071 At special positions: 0 Unit cell: (204.12, 189, 155.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 208 16.00 P 29 15.00 O 7479 8.00 N 6871 7.00 C 24484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 5 192 " - pdb=" SG CYS 5 202 " distance=2.04 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.85 Conformation dependent library (CDL) restraints added in 6.6 seconds 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9300 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 28 sheets defined 31.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.43 Creating SS restraints... Processing helix chain '3' and resid 7 through 19 removed outlier: 3.589A pdb=" N ASP 3 18 " --> pdb=" O GLU 3 15 " (cutoff:3.500A) Processing helix chain '3' and resid 23 through 28 Processing helix chain '3' and resid 48 through 54 Processing helix chain '3' and resid 56 through 64 removed outlier: 4.212A pdb=" N LEU 3 62 " --> pdb=" O ARG 3 58 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU 3 63 " --> pdb=" O ALA 3 59 " (cutoff:3.500A) Processing helix chain '3' and resid 70 through 84 Processing helix chain '3' and resid 87 through 89 No H-bonds generated for 'chain '3' and resid 87 through 89' Processing helix chain '3' and resid 202 through 204 No H-bonds generated for 'chain '3' and resid 202 through 204' Processing helix chain '3' and resid 275 through 283 Processing helix chain '3' and resid 288 through 295 removed outlier: 4.338A pdb=" N PHE 3 291 " --> pdb=" O ASN 3 288 " (cutoff:3.500A) Processing helix chain '3' and resid 309 through 316 removed outlier: 4.749A pdb=" N CYS 3 314 " --> pdb=" O GLN 3 310 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU 3 315 " --> pdb=" O ALA 3 311 " (cutoff:3.500A) Processing helix chain '3' and resid 350 through 354 Processing helix chain '3' and resid 411 through 423 removed outlier: 4.006A pdb=" N THR 3 415 " --> pdb=" O ASP 3 411 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA 3 416 " --> pdb=" O ILE 3 412 " (cutoff:3.500A) Processing helix chain '3' and resid 487 through 502 removed outlier: 3.938A pdb=" N MET 3 491 " --> pdb=" O ASP 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 559 through 567 removed outlier: 4.393A pdb=" N TYR 3 565 " --> pdb=" O PHE 3 561 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE 3 566 " --> pdb=" O MET 3 562 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS 3 567 " --> pdb=" O ARG 3 563 " (cutoff:3.500A) Processing helix chain '3' and resid 569 through 571 No H-bonds generated for 'chain '3' and resid 569 through 571' Processing helix chain '3' and resid 580 through 594 Processing helix chain '3' and resid 601 through 603 No H-bonds generated for 'chain '3' and resid 601 through 603' Processing helix chain '3' and resid 609 through 623 removed outlier: 3.764A pdb=" N GLU 3 613 " --> pdb=" O ARG 3 610 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU 3 615 " --> pdb=" O LEU 3 612 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU 3 618 " --> pdb=" O LEU 3 615 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR 3 620 " --> pdb=" O ARG 3 617 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS 3 622 " --> pdb=" O SER 3 619 " (cutoff:3.500A) Processing helix chain '3' and resid 633 through 639 Processing helix chain '3' and resid 641 through 647 removed outlier: 3.908A pdb=" N TYR 3 647 " --> pdb=" O VAL 3 643 " (cutoff:3.500A) Processing helix chain '4' and resid 161 through 173 Processing helix chain '4' and resid 178 through 181 No H-bonds generated for 'chain '4' and resid 178 through 181' Processing helix chain '4' and resid 195 through 204 Processing helix chain '4' and resid 216 through 219 removed outlier: 3.674A pdb=" N LYS 4 219 " --> pdb=" O ALA 4 216 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 216 through 219' Processing helix chain '4' and resid 224 through 231 Processing helix chain '4' and resid 237 through 251 removed outlier: 4.679A pdb=" N PHE 4 249 " --> pdb=" O ASN 4 245 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU 4 250 " --> pdb=" O GLU 4 246 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG 4 251 " --> pdb=" O MET 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 446 through 456 removed outlier: 4.488A pdb=" N ALA 4 455 " --> pdb=" O GLN 4 452 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS 4 456 " --> pdb=" O LEU 4 453 " (cutoff:3.500A) Processing helix chain '4' and resid 458 through 468 removed outlier: 3.853A pdb=" N TYR 4 461 " --> pdb=" O PRO 4 458 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LEU 4 464 " --> pdb=" O TYR 4 461 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE 4 468 " --> pdb=" O ALA 4 465 " (cutoff:3.500A) Processing helix chain '4' and resid 476 through 486 removed outlier: 3.990A pdb=" N LYS 4 480 " --> pdb=" O ASP 4 477 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU 4 484 " --> pdb=" O GLY 4 481 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU 4 486 " --> pdb=" O LEU 4 483 " (cutoff:3.500A) Processing helix chain '4' and resid 518 through 528 removed outlier: 3.651A pdb=" N LEU 4 522 " --> pdb=" O LYS 4 518 " (cutoff:3.500A) Processing helix chain '4' and resid 578 through 580 No H-bonds generated for 'chain '4' and resid 578 through 580' Processing helix chain '4' and resid 632 through 635 No H-bonds generated for 'chain '4' and resid 632 through 635' Processing helix chain '4' and resid 659 through 669 removed outlier: 4.171A pdb=" N ARG 4 663 " --> pdb=" O ILE 4 659 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU 4 664 " --> pdb=" O PHE 4 660 " (cutoff:3.500A) Processing helix chain '4' and resid 671 through 674 No H-bonds generated for 'chain '4' and resid 671 through 674' Processing helix chain '4' and resid 690 through 697 Processing helix chain '4' and resid 710 through 723 removed outlier: 3.845A pdb=" N GLN 4 714 " --> pdb=" O GLN 4 710 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL 4 717 " --> pdb=" O ILE 4 713 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP 4 718 " --> pdb=" O GLN 4 714 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL 4 722 " --> pdb=" O ASP 4 718 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLY 4 723 " --> pdb=" O MET 4 719 " (cutoff:3.500A) Processing helix chain '4' and resid 735 through 748 removed outlier: 3.680A pdb=" N ALA 4 745 " --> pdb=" O ARG 4 741 " (cutoff:3.500A) Processing helix chain '4' and resid 758 through 767 Processing helix chain '7' and resid 8 through 18 Processing helix chain '7' and resid 32 through 40 Processing helix chain '7' and resid 52 through 58 removed outlier: 4.194A pdb=" N GLU 7 57 " --> pdb=" O ASP 7 53 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE 7 58 " --> pdb=" O ASP 7 54 " (cutoff:3.500A) Processing helix chain '7' and resid 72 through 83 removed outlier: 3.668A pdb=" N ILE 7 81 " --> pdb=" O PHE 7 77 " (cutoff:3.500A) Processing helix chain '7' and resid 99 through 106 removed outlier: 3.934A pdb=" N GLU 7 104 " --> pdb=" O ASP 7 100 " (cutoff:3.500A) Processing helix chain '7' and resid 224 through 226 No H-bonds generated for 'chain '7' and resid 224 through 226' Processing helix chain '7' and resid 259 through 261 No H-bonds generated for 'chain '7' and resid 259 through 261' Processing helix chain '7' and resid 322 through 329 removed outlier: 4.584A pdb=" N GLU 7 325 " --> pdb=" O GLU 7 322 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA 7 328 " --> pdb=" O GLU 7 325 " (cutoff:3.500A) Processing helix chain '7' and resid 335 through 339 Processing helix chain '7' and resid 348 through 359 Processing helix chain '7' and resid 366 through 368 No H-bonds generated for 'chain '7' and resid 366 through 368' Processing helix chain '7' and resid 387 through 397 removed outlier: 4.100A pdb=" N LEU 7 391 " --> pdb=" O LYS 7 387 " (cutoff:3.500A) Processing helix chain '7' and resid 433 through 436 No H-bonds generated for 'chain '7' and resid 433 through 436' Processing helix chain '7' and resid 447 through 449 No H-bonds generated for 'chain '7' and resid 447 through 449' Processing helix chain '7' and resid 453 through 462 removed outlier: 3.756A pdb=" N THR 7 456 " --> pdb=" O GLN 7 453 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU 7 460 " --> pdb=" O ALA 7 457 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL 7 461 " --> pdb=" O ILE 7 458 " (cutoff:3.500A) Processing helix chain '7' and resid 509 through 513 Processing helix chain '7' and resid 529 through 542 removed outlier: 3.535A pdb=" N ILE 7 537 " --> pdb=" O LEU 7 533 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL 7 540 " --> pdb=" O HIS 7 536 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS 7 541 " --> pdb=" O ILE 7 537 " (cutoff:3.500A) Processing helix chain '7' and resid 556 through 565 removed outlier: 3.692A pdb=" N LEU 7 565 " --> pdb=" O ARG 7 561 " (cutoff:3.500A) Processing helix chain '7' and resid 575 through 591 removed outlier: 4.261A pdb=" N ASP 7 579 " --> pdb=" O GLU 7 576 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE 7 581 " --> pdb=" O THR 7 578 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR 7 585 " --> pdb=" O VAL 7 582 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU 7 591 " --> pdb=" O LEU 7 588 " (cutoff:3.500A) Processing helix chain '7' and resid 603 through 620 removed outlier: 4.512A pdb=" N LEU 7 607 " --> pdb=" O ALA 7 603 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE 7 609 " --> pdb=" O ASN 7 605 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA 7 617 " --> pdb=" O SER 7 613 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG 7 618 " --> pdb=" O THR 7 614 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU 7 619 " --> pdb=" O ALA 7 615 " (cutoff:3.500A) Processing helix chain '7' and resid 627 through 640 removed outlier: 3.520A pdb=" N GLU 7 632 " --> pdb=" O ASP 7 628 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA 7 633 " --> pdb=" O ASP 7 629 " (cutoff:3.500A) Processing helix chain '6' and resid 14 through 29 removed outlier: 3.578A pdb=" N LEU 6 24 " --> pdb=" O ALA 6 21 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP 6 27 " --> pdb=" O LEU 6 24 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE 6 28 " --> pdb=" O PHE 6 25 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 48 removed outlier: 3.764A pdb=" N GLU 6 48 " --> pdb=" O ALA 6 44 " (cutoff:3.500A) Processing helix chain '6' and resid 60 through 64 Processing helix chain '6' and resid 70 through 73 No H-bonds generated for 'chain '6' and resid 70 through 73' Processing helix chain '6' and resid 77 through 94 Proline residue: 6 82 - end of helix Processing helix chain '6' and resid 122 through 124 No H-bonds generated for 'chain '6' and resid 122 through 124' Processing helix chain '6' and resid 224 through 226 No H-bonds generated for 'chain '6' and resid 224 through 226' Processing helix chain '6' and resid 324 through 332 removed outlier: 4.607A pdb=" N HIS 6 327 " --> pdb=" O ALA 6 324 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR 6 330 " --> pdb=" O HIS 6 327 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU 6 331 " --> pdb=" O LYS 6 328 " (cutoff:3.500A) Processing helix chain '6' and resid 337 through 344 Processing helix chain '6' and resid 356 through 359 No H-bonds generated for 'chain '6' and resid 356 through 359' Processing helix chain '6' and resid 361 through 364 Processing helix chain '6' and resid 398 through 404 removed outlier: 3.550A pdb=" N SER 6 402 " --> pdb=" O LEU 6 398 " (cutoff:3.500A) Processing helix chain '6' and resid 461 through 468 removed outlier: 4.193A pdb=" N GLU 6 467 " --> pdb=" O VAL 6 463 " (cutoff:3.500A) Processing helix chain '6' and resid 508 through 512 Processing helix chain '6' and resid 517 through 521 removed outlier: 3.935A pdb=" N ARG 6 521 " --> pdb=" O ILE 6 518 " (cutoff:3.500A) Processing helix chain '6' and resid 534 through 544 removed outlier: 3.613A pdb=" N ILE 6 540 " --> pdb=" O VAL 6 536 " (cutoff:3.500A) Processing helix chain '6' and resid 561 through 572 removed outlier: 4.409A pdb=" N THR 6 569 " --> pdb=" O LEU 6 565 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE 6 570 " --> pdb=" O ARG 6 566 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG 6 572 " --> pdb=" O VAL 6 568 " (cutoff:3.500A) Processing helix chain '6' and resid 581 through 597 removed outlier: 4.503A pdb=" N VAL 6 587 " --> pdb=" O GLY 6 583 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLU 6 588 " --> pdb=" O HIS 6 584 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG 6 596 " --> pdb=" O HIS 6 592 " (cutoff:3.500A) Processing helix chain '6' and resid 610 through 626 Processing helix chain '6' and resid 634 through 651 removed outlier: 3.642A pdb=" N LEU 6 643 " --> pdb=" O ALA 6 640 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU 6 644 " --> pdb=" O PHE 6 641 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE 6 648 " --> pdb=" O ASN 6 645 " (cutoff:3.500A) Processing helix chain '5' and resid 28 through 31 No H-bonds generated for 'chain '5' and resid 28 through 31' Processing helix chain '5' and resid 33 through 40 Processing helix chain '5' and resid 53 through 57 Processing helix chain '5' and resid 72 through 75 No H-bonds generated for 'chain '5' and resid 72 through 75' Processing helix chain '5' and resid 80 through 83 No H-bonds generated for 'chain '5' and resid 80 through 83' Processing helix chain '5' and resid 87 through 105 removed outlier: 4.069A pdb=" N GLU 5 92 " --> pdb=" O THR 5 88 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP 5 103 " --> pdb=" O ARG 5 99 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) Processing helix chain '5' and resid 137 through 139 No H-bonds generated for 'chain '5' and resid 137 through 139' Processing helix chain '5' and resid 211 through 213 No H-bonds generated for 'chain '5' and resid 211 through 213' Processing helix chain '5' and resid 313 through 323 removed outlier: 3.612A pdb=" N MET 5 322 " --> pdb=" O HIS 5 318 " (cutoff:3.500A) Processing helix chain '5' and resid 331 through 334 removed outlier: 4.007A pdb=" N GLN 5 334 " --> pdb=" O ARG 5 331 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 331 through 334' Processing helix chain '5' and resid 344 through 350 removed outlier: 3.875A pdb=" N ALA 5 349 " --> pdb=" O ASP 5 345 " (cutoff:3.500A) Processing helix chain '5' and resid 384 through 389 removed outlier: 3.583A pdb=" N LEU 5 388 " --> pdb=" O LYS 5 384 " (cutoff:3.500A) Processing helix chain '5' and resid 420 through 422 No H-bonds generated for 'chain '5' and resid 420 through 422' Processing helix chain '5' and resid 453 through 459 removed outlier: 4.572A pdb=" N ALA 5 458 " --> pdb=" O ALA 5 454 " (cutoff:3.500A) Processing helix chain '5' and resid 490 through 494 Processing helix chain '5' and resid 506 through 508 No H-bonds generated for 'chain '5' and resid 506 through 508' Processing helix chain '5' and resid 523 through 531 removed outlier: 3.671A pdb=" N ILE 5 527 " --> pdb=" O GLU 5 523 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR 5 528 " --> pdb=" O SER 5 524 " (cutoff:3.500A) Processing helix chain '5' and resid 534 through 537 No H-bonds generated for 'chain '5' and resid 534 through 537' Processing helix chain '5' and resid 555 through 567 removed outlier: 5.551A pdb=" N THR 5 567 " --> pdb=" O HIS 5 563 " (cutoff:3.500A) Processing helix chain '5' and resid 609 through 625 removed outlier: 7.034A pdb=" N VAL 5 615 " --> pdb=" O ARG 5 610 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE 5 616 " --> pdb=" O GLN 5 611 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ARG 5 617 " --> pdb=" O LEU 5 612 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE 5 618 " --> pdb=" O GLU 5 613 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA 5 623 " --> pdb=" O SER 5 619 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS 5 624 " --> pdb=" O GLU 5 620 " (cutoff:3.500A) Processing helix chain '5' and resid 638 through 650 removed outlier: 4.253A pdb=" N VAL 5 645 " --> pdb=" O ARG 5 641 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER 5 646 " --> pdb=" O LEU 5 642 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU 5 648 " --> pdb=" O GLN 5 644 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP 5 649 " --> pdb=" O VAL 5 645 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA 5 650 " --> pdb=" O SER 5 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 13 No H-bonds generated for 'chain 'A' and resid 10 through 13' Processing helix chain 'A' and resid 28 through 42 removed outlier: 4.206A pdb=" N ILE A 35 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 62 removed outlier: 3.972A pdb=" N LYS A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 106 through 109 No H-bonds generated for 'chain 'A' and resid 106 through 109' Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.824A pdb=" N LEU A 185 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 186 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER A 195 " --> pdb=" O GLN A 192 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU A 196 " --> pdb=" O TRP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 removed outlier: 3.877A pdb=" N LYS A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.741A pdb=" N TRP A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 238 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 239 " --> pdb=" O TRP A 235 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 removed outlier: 5.287A pdb=" N GLU A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 4.341A pdb=" N ARG A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 removed outlier: 4.019A pdb=" N GLN A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 removed outlier: 4.238A pdb=" N GLU A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 347 through 360 removed outlier: 4.751A pdb=" N PHE A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N SER A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 358 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.717A pdb=" N LEU A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 395 " --> pdb=" O TYR A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 395' Processing helix chain 'A' and resid 405 through 414 removed outlier: 3.702A pdb=" N SER A 414 " --> pdb=" O PHE A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 442 removed outlier: 4.006A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE A 440 " --> pdb=" O HIS A 436 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 447 No H-bonds generated for 'chain 'A' and resid 444 through 447' Processing helix chain 'A' and resid 468 through 471 No H-bonds generated for 'chain 'A' and resid 468 through 471' Processing helix chain 'A' and resid 474 through 483 removed outlier: 3.928A pdb=" N LEU A 479 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 483 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 534 through 541 removed outlier: 3.934A pdb=" N ALA A 538 " --> pdb=" O PHE A 535 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN A 540 " --> pdb=" O GLN A 537 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 541 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'H' and resid 11 through 17 removed outlier: 3.959A pdb=" N LEU H 16 " --> pdb=" O PHE H 13 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS H 17 " --> pdb=" O ASP H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 39 Processing helix chain 'H' and resid 45 through 48 No H-bonds generated for 'chain 'H' and resid 45 through 48' Processing helix chain 'H' and resid 61 through 98 Proline residue: H 65 - end of helix removed outlier: 3.827A pdb=" N ASN H 68 " --> pdb=" O PRO H 65 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA H 72 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA H 73 " --> pdb=" O ARG H 70 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG H 76 " --> pdb=" O ALA H 73 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS H 78 " --> pdb=" O GLN H 75 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG H 79 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS H 80 " --> pdb=" O ASN H 77 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU H 82 " --> pdb=" O ARG H 79 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR H 84 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU H 87 " --> pdb=" O TYR H 84 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG H 90 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG H 91 " --> pdb=" O ARG H 88 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE H 92 " --> pdb=" O CYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 125 Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'L' and resid 10 through 12 No H-bonds generated for 'chain 'L' and resid 10 through 12' Processing helix chain 'L' and resid 50 through 53 No H-bonds generated for 'chain 'L' and resid 50 through 53' Processing helix chain 'L' and resid 74 through 80 removed outlier: 5.397A pdb=" N LYS L 79 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ARG L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 105 Proline residue: L 104 - end of helix Processing helix chain 'L' and resid 112 through 126 removed outlier: 3.667A pdb=" N LYS L 118 " --> pdb=" O ARG L 114 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU L 125 " --> pdb=" O PHE L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 134 Processing helix chain 'L' and resid 153 through 157 Processing helix chain 'L' and resid 161 through 168 removed outlier: 3.852A pdb=" N ASP L 165 " --> pdb=" O PRO L 161 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N HIS L 166 " --> pdb=" O TYR L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 175 removed outlier: 3.852A pdb=" N THR L 175 " --> pdb=" O ARG L 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 172 through 175' Processing helix chain 'M' and resid 56 through 59 Processing helix chain 'M' and resid 79 through 85 removed outlier: 4.624A pdb=" N VAL M 84 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 111 removed outlier: 4.328A pdb=" N THR M 109 " --> pdb=" O GLY M 105 " (cutoff:3.500A) Proline residue: M 110 - end of helix Processing helix chain 'M' and resid 118 through 130 removed outlier: 3.945A pdb=" N PHE M 122 " --> pdb=" O GLY M 118 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU M 123 " --> pdb=" O ARG M 119 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR M 124 " --> pdb=" O ILE M 120 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU M 125 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG M 128 " --> pdb=" O THR M 124 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL M 129 " --> pdb=" O LEU M 125 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG M 130 " --> pdb=" O ARG M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 171 removed outlier: 3.974A pdb=" N ASN M 164 " --> pdb=" O GLY M 160 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU M 169 " --> pdb=" O SER M 165 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU M 171 " --> pdb=" O TYR M 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 50 removed outlier: 5.664A pdb=" N THR N 44 " --> pdb=" O ILE N 41 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA N 45 " --> pdb=" O ILE N 42 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN N 48 " --> pdb=" O ALA N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 78 removed outlier: 5.690A pdb=" N MET N 66 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL N 67 " --> pdb=" O GLU N 64 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN N 69 " --> pdb=" O MET N 66 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL N 70 " --> pdb=" O VAL N 67 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS N 72 " --> pdb=" O GLN N 69 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU N 75 " --> pdb=" O HIS N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 96 removed outlier: 3.529A pdb=" N HIS N 90 " --> pdb=" O ARG N 86 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER N 91 " --> pdb=" O ALA N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 114 removed outlier: 3.911A pdb=" N SER N 103 " --> pdb=" O TYR N 99 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU N 105 " --> pdb=" O MET N 101 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS N 107 " --> pdb=" O SER N 103 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG N 108 " --> pdb=" O TYR N 104 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN N 110 " --> pdb=" O ARG N 106 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE N 112 " --> pdb=" O ARG N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 123 Processing helix chain 'N' and resid 135 through 154 removed outlier: 3.864A pdb=" N PHE N 140 " --> pdb=" O GLU N 137 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN N 142 " --> pdb=" O LYS N 139 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA N 145 " --> pdb=" O GLN N 142 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN N 147 " --> pdb=" O PHE N 144 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU N 150 " --> pdb=" O ASN N 147 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N TYR N 151 " --> pdb=" O VAL N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 219 through 222 No H-bonds generated for 'chain 'N' and resid 219 through 222' Processing helix chain '2' and resid 176 through 185 removed outlier: 4.168A pdb=" N ALA 2 181 " --> pdb=" O THR 2 178 " (cutoff:3.500A) Processing helix chain '2' and resid 199 through 210 removed outlier: 3.720A pdb=" N ILE 2 204 " --> pdb=" O TYR 2 200 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG 2 205 " --> pdb=" O ARG 2 201 " (cutoff:3.500A) Processing helix chain '2' and resid 219 through 225 Processing helix chain '2' and resid 237 through 255 removed outlier: 3.528A pdb=" N LEU 2 241 " --> pdb=" O PRO 2 237 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL 2 247 " --> pdb=" O ILE 2 243 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER 2 254 " --> pdb=" O ASP 2 250 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE 2 255 " --> pdb=" O MET 2 251 " (cutoff:3.500A) Processing helix chain '2' and resid 447 through 450 No H-bonds generated for 'chain '2' and resid 447 through 450' Processing helix chain '2' and resid 456 through 464 removed outlier: 3.611A pdb=" N VAL 2 459 " --> pdb=" O PRO 2 456 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG 2 461 " --> pdb=" O ILE 2 458 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL 2 462 " --> pdb=" O VAL 2 459 " (cutoff:3.500A) Processing helix chain '2' and resid 474 through 485 removed outlier: 4.256A pdb=" N LEU 2 482 " --> pdb=" O ARG 2 478 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA 2 483 " --> pdb=" O ALA 2 479 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU 2 484 " --> pdb=" O LEU 2 480 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N PHE 2 485 " --> pdb=" O ALA 2 481 " (cutoff:3.500A) Processing helix chain '2' and resid 520 through 524 Processing helix chain '2' and resid 579 through 590 removed outlier: 3.886A pdb=" N SER 2 584 " --> pdb=" O GLN 2 580 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE 2 585 " --> pdb=" O ASP 2 581 " (cutoff:3.500A) Processing helix chain '2' and resid 636 through 641 removed outlier: 4.057A pdb=" N SER 2 640 " --> pdb=" O GLU 2 636 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ARG 2 641 " --> pdb=" O PRO 2 637 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 636 through 641' Processing helix chain '2' and resid 654 through 669 Processing helix chain '2' and resid 697 through 707 removed outlier: 4.692A pdb=" N ALA 2 704 " --> pdb=" O ILE 2 701 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS 2 705 " --> pdb=" O VAL 2 702 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN 2 707 " --> pdb=" O ALA 2 704 " (cutoff:3.500A) Processing helix chain '2' and resid 717 through 729 removed outlier: 5.385A pdb=" N GLN 2 726 " --> pdb=" O MET 2 723 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU 2 727 " --> pdb=" O TYR 2 724 " (cutoff:3.500A) Processing helix chain '2' and resid 742 through 756 removed outlier: 4.328A pdb=" N VAL 2 747 " --> pdb=" O HIS 2 743 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU 2 752 " --> pdb=" O ILE 2 748 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA 2 753 " --> pdb=" O ARG 2 749 " (cutoff:3.500A) Processing helix chain '2' and resid 765 through 782 removed outlier: 3.696A pdb=" N MET 2 774 " --> pdb=" O MET 2 770 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE 2 780 " --> pdb=" O LEU 2 776 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU 2 781 " --> pdb=" O GLU 2 777 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA 2 782 " --> pdb=" O SER 2 778 " (cutoff:3.500A) Processing helix chain '2' and resid 789 through 794 Processing sheet with id= A, first strand: chain '3' and resid 107 through 109 removed outlier: 6.336A pdb=" N CYS 3 123 " --> pdb=" O VAL 3 108 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE 3 234 " --> pdb=" O VAL 3 124 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY 3 126 " --> pdb=" O VAL 3 232 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '3' and resid 127 through 129 removed outlier: 3.942A pdb=" N GLN 3 194 " --> pdb=" O CYS 3 218 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU 3 196 " --> pdb=" O ILE 3 216 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '3' and resid 135 through 138 Processing sheet with id= D, first strand: chain '3' and resid 140 through 143 Processing sheet with id= E, first strand: chain '3' and resid 237 through 239 removed outlier: 3.913A pdb=" N VAL 3 256 " --> pdb=" O ARG 3 239 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 426 through 428 removed outlier: 3.820A pdb=" N VAL 3 426 " --> pdb=" O LEU 3 437 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU 3 437 " --> pdb=" O VAL 3 426 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '4' and resid 285 through 291 removed outlier: 3.602A pdb=" N GLY 4 290 " --> pdb=" O VAL 4 391 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '4' and resid 304 through 306 Processing sheet with id= I, first strand: chain '4' and resid 354 through 358 Processing sheet with id= J, first strand: chain '4' and resid 397 through 400 Processing sheet with id= K, first strand: chain '7' and resid 232 through 235 removed outlier: 3.743A pdb=" N CYS 7 257 " --> pdb=" O GLN 7 233 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL 7 235 " --> pdb=" O ILE 7 255 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '7' and resid 376 through 380 removed outlier: 5.902A pdb=" N ILE 7 484 " --> pdb=" O ILE 7 377 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU 7 379 " --> pdb=" O ILE 7 484 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA 7 486 " --> pdb=" O LEU 7 379 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU 7 485 " --> pdb=" O CYS 7 442 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN 7 402 " --> pdb=" O VAL 7 441 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS 7 443 " --> pdb=" O GLN 7 402 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '7' and resid 176 through 179 removed outlier: 7.399A pdb=" N LYS 7 228 " --> pdb=" O VAL 7 178 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '6' and resid 56 through 58 removed outlier: 6.319A pdb=" N ALA 6 107 " --> pdb=" O VAL 6 57 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain '6' and resid 198 through 202 removed outlier: 3.548A pdb=" N GLN 6 198 " --> pdb=" O LEU 6 222 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU 6 222 " --> pdb=" O GLN 6 198 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE 6 220 " --> pdb=" O ILE 6 200 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '6' and resid 408 through 412 removed outlier: 7.388A pdb=" N ILE 6 448 " --> pdb=" O ILE 6 409 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR 6 411 " --> pdb=" O ILE 6 448 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS 6 450 " --> pdb=" O THR 6 411 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '5' and resid 223 through 225 removed outlier: 3.559A pdb=" N LEU 5 224 " --> pdb=" O LEU 5 240 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU 5 240 " --> pdb=" O LEU 5 224 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain '5' and resid 374 through 378 removed outlier: 5.785A pdb=" N MET 5 513 " --> pdb=" O LEU 5 375 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU 5 377 " --> pdb=" O MET 5 513 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE 5 515 " --> pdb=" O LEU 5 377 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain '5' and resid 439 through 442 Processing sheet with id= T, first strand: chain 'A' and resid 71 through 74 removed outlier: 6.575A pdb=" N THR A 94 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU A 74 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N PHE A 96 " --> pdb=" O LEU A 74 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'A' and resid 284 through 289 removed outlier: 4.039A pdb=" N THR A 284 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 375 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 501 through 505 Processing sheet with id= W, first strand: chain 'L' and resid 14 through 18 Processing sheet with id= X, first strand: chain '2' and resid 215 through 218 Processing sheet with id= Y, first strand: chain '2' and resid 303 through 305 Processing sheet with id= Z, first strand: chain '2' and resid 380 through 382 removed outlier: 3.623A pdb=" N ILE 2 425 " --> pdb=" O ILE 2 402 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE 2 402 " --> pdb=" O ILE 2 425 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain '2' and resid 397 through 399 Processing sheet with id= AB, first strand: chain '2' and resid 504 through 507 removed outlier: 5.987A pdb=" N VAL 2 644 " --> pdb=" O LEU 2 505 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N CYS 2 507 " --> pdb=" O VAL 2 644 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS 2 646 " --> pdb=" O CYS 2 507 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB 724 hydrogen bonds defined for protein. 1620 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: 10.28 Time building geometry restraints manager: 17.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 6662 1.31 - 1.44: 9992 1.44 - 1.57: 22634 1.57 - 1.70: 120 1.70 - 1.83: 336 Bond restraints: 39744 Sorted by residual: bond pdb=" C THR 7 254 " pdb=" N ILE 7 255 " ideal model delta sigma weight residual 1.331 1.667 -0.336 1.32e-02 5.74e+03 6.50e+02 bond pdb=" C VAL 4 588 " pdb=" N LEU 4 589 " ideal model delta sigma weight residual 1.332 1.659 -0.326 1.40e-02 5.10e+03 5.44e+02 bond pdb=" C PHE 6 108 " pdb=" N THR 6 109 " ideal model delta sigma weight residual 1.328 1.523 -0.194 1.23e-02 6.61e+03 2.50e+02 bond pdb=" C PRO 7 267 " pdb=" N GLY 7 268 " ideal model delta sigma weight residual 1.331 1.536 -0.205 1.46e-02 4.69e+03 1.98e+02 bond pdb=" C THR 4 271 " pdb=" N ARG 4 272 " ideal model delta sigma weight residual 1.332 1.487 -0.155 1.29e-02 6.01e+03 1.44e+02 ... (remaining 39739 not shown) Histogram of bond angle deviations from ideal: 84.50 - 98.75: 32 98.75 - 113.01: 20863 113.01 - 127.27: 32412 127.27 - 141.53: 425 141.53 - 155.79: 5 Bond angle restraints: 53737 Sorted by residual: angle pdb=" PB ATP 3 901 " pdb=" O3B ATP 3 901 " pdb=" PG ATP 3 901 " ideal model delta sigma weight residual 139.87 115.04 24.83 1.00e+00 1.00e+00 6.16e+02 angle pdb=" PB ATP 2 901 " pdb=" O3B ATP 2 901 " pdb=" PG ATP 2 901 " ideal model delta sigma weight residual 139.87 116.06 23.81 1.00e+00 1.00e+00 5.67e+02 angle pdb=" PA ATP 3 901 " pdb=" O3A ATP 3 901 " pdb=" PB ATP 3 901 " ideal model delta sigma weight residual 136.83 113.35 23.48 1.00e+00 1.00e+00 5.51e+02 angle pdb=" PB ATP 4 901 " pdb=" O3B ATP 4 901 " pdb=" PG ATP 4 901 " ideal model delta sigma weight residual 139.87 117.24 22.63 1.00e+00 1.00e+00 5.12e+02 angle pdb=" PB ATP 6 901 " pdb=" O3B ATP 6 901 " pdb=" PG ATP 6 901 " ideal model delta sigma weight residual 139.87 118.05 21.82 1.00e+00 1.00e+00 4.76e+02 ... (remaining 53732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 23465 35.47 - 70.94: 896 70.94 - 106.41: 81 106.41 - 141.88: 7 141.88 - 177.36: 2 Dihedral angle restraints: 24451 sinusoidal: 10166 harmonic: 14285 Sorted by residual: dihedral pdb=" C PRO 5 419 " pdb=" N PRO 5 419 " pdb=" CA PRO 5 419 " pdb=" CB PRO 5 419 " ideal model delta harmonic sigma weight residual -120.70 -153.65 32.95 0 2.50e+00 1.60e-01 1.74e+02 dihedral pdb=" CD ARG 6 427 " pdb=" NE ARG 6 427 " pdb=" CZ ARG 6 427 " pdb=" NH1 ARG 6 427 " ideal model delta sinusoidal sigma weight residual 0.00 119.81 -119.81 1 1.00e+01 1.00e-02 1.44e+02 dihedral pdb=" N PRO 5 419 " pdb=" C PRO 5 419 " pdb=" CA PRO 5 419 " pdb=" CB PRO 5 419 " ideal model delta harmonic sigma weight residual 115.10 145.01 -29.91 0 2.50e+00 1.60e-01 1.43e+02 ... (remaining 24448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.584: 6043 0.584 - 1.168: 8 1.168 - 1.752: 17 1.752 - 2.336: 14 2.336 - 2.920: 1 Chirality restraints: 6083 Sorted by residual: chirality pdb=" CB VAL 4 652 " pdb=" CA VAL 4 652 " pdb=" CG1 VAL 4 652 " pdb=" CG2 VAL 4 652 " both_signs ideal model delta sigma weight residual False -2.63 0.29 -2.92 2.00e-01 2.50e+01 2.13e+02 chirality pdb=" CB ILE 4 472 " pdb=" CA ILE 4 472 " pdb=" CG1 ILE 4 472 " pdb=" CG2 ILE 4 472 " both_signs ideal model delta sigma weight residual False 2.64 0.31 2.33 2.00e-01 2.50e+01 1.36e+02 chirality pdb=" CB ILE 2 310 " pdb=" CA ILE 2 310 " pdb=" CG1 ILE 2 310 " pdb=" CG2 ILE 2 310 " both_signs ideal model delta sigma weight residual False 2.64 0.49 2.15 2.00e-01 2.50e+01 1.16e+02 ... (remaining 6080 not shown) Planarity restraints: 6914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 5 510 " 0.443 9.50e-02 1.11e+02 2.26e-01 1.69e+02 pdb=" NE ARG 5 510 " -0.102 2.00e-02 2.50e+03 pdb=" CZ ARG 5 510 " 0.202 2.00e-02 2.50e+03 pdb=" NH1 ARG 5 510 " -0.069 2.00e-02 2.50e+03 pdb=" NH2 ARG 5 510 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 641 " 0.459 9.50e-02 1.11e+02 2.29e-01 1.54e+02 pdb=" NE ARG 2 641 " -0.099 2.00e-02 2.50e+03 pdb=" CZ ARG 2 641 " 0.190 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 641 " -0.061 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 641 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP 7 629 " 0.070 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C ASP 7 629 " -0.211 2.00e-02 2.50e+03 pdb=" O ASP 7 629 " 0.067 2.00e-02 2.50e+03 pdb=" N VAL 7 630 " 0.075 2.00e-02 2.50e+03 ... (remaining 6911 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.80: 4 1.80 - 2.58: 760 2.58 - 3.35: 53884 3.35 - 4.13: 93384 4.13 - 4.90: 156573 Nonbonded interactions: 304605 Sorted by model distance: nonbonded pdb=" NH2 ARG 7 219 " pdb=" CD ARG 6 263 " model vdw 1.031 3.520 nonbonded pdb=" NH2 ARG 7 219 " pdb=" CG ARG 6 263 " model vdw 1.233 3.520 nonbonded pdb=" OD2 ASP 3 397 " pdb=" CG1 VAL 7 246 " model vdw 1.371 3.460 nonbonded pdb=" O VAL 5 425 " pdb=" CG2 VAL 5 425 " model vdw 1.780 3.460 nonbonded pdb=" NZ LYS 5 384 " pdb=" OD1 ASN 5 486 " model vdw 1.918 2.520 ... (remaining 304600 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.970 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: 13.620 Check model and map are aligned: 0.570 Set scattering table: 0.340 Process input model: 93.200 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.140 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 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 : 0.013 0.336 39744 Z= 0.836 Angle : 1.770 34.092 53737 Z= 1.007 Chirality : 0.162 2.920 6083 Planarity : 0.018 0.488 6914 Dihedral : 18.627 177.356 15148 Min Nonbonded Distance : 1.031 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.77 % Allowed : 17.40 % Favored : 81.82 % Rotamer: Outliers : 7.45 % Allowed : 16.00 % Favored : 76.55 % Cbeta Deviations : 0.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.99 % 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: -5.68 (0.09), residues: 4775 helix: -3.73 (0.09), residues: 1355 sheet: -3.86 (0.19), residues: 398 loop : -4.01 (0.09), residues: 3022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP 2 554 HIS 0.043 0.005 HIS L 91 PHE 0.061 0.005 PHE 5 219 TYR 0.053 0.005 TYR L 30 ARG 0.208 0.005 ARG 5 510 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1441 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 1127 time to evaluate : 4.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 70 GLN cc_start: 0.8515 (mt0) cc_final: 0.8221 (mm-40) REVERT: 3 79 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8175 (tm-30) REVERT: 3 118 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6339 (mt) REVERT: 3 130 LYS cc_start: 0.5206 (mtpt) cc_final: 0.4135 (mptt) REVERT: 3 197 THR cc_start: 0.3487 (p) cc_final: 0.3233 (p) REVERT: 3 218 CYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7950 (t) REVERT: 3 230 ASP cc_start: 0.6160 (t0) cc_final: 0.5902 (t0) REVERT: 3 239 ARG cc_start: 0.7188 (mtt180) cc_final: 0.6202 (mtp-110) REVERT: 3 409 MET cc_start: 0.6561 (ttt) cc_final: 0.6351 (ttt) REVERT: 3 419 GLU cc_start: 0.7525 (tt0) cc_final: 0.7146 (tm-30) REVERT: 3 448 ASN cc_start: 0.6314 (t0) cc_final: 0.5961 (m-40) REVERT: 3 628 SER cc_start: 0.6688 (m) cc_final: 0.6473 (m) REVERT: 4 210 TYR cc_start: 0.6703 (m-80) cc_final: 0.5933 (m-80) REVERT: 4 285 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7442 (pt) REVERT: 4 299 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7653 (tp) REVERT: 4 306 PHE cc_start: 0.6009 (t80) cc_final: 0.5752 (t80) REVERT: 4 324 ARG cc_start: 0.6508 (mpp-170) cc_final: 0.6095 (mmm160) REVERT: 4 356 LYS cc_start: 0.8021 (ttmm) cc_final: 0.7695 (tttp) REVERT: 4 363 ASP cc_start: 0.7143 (m-30) cc_final: 0.6820 (t0) REVERT: 4 371 HIS cc_start: 0.6506 (m-70) cc_final: 0.5642 (m-70) REVERT: 4 372 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8224 (p0) REVERT: 4 373 VAL cc_start: 0.5951 (OUTLIER) cc_final: 0.5740 (p) REVERT: 4 428 ASP cc_start: -0.0269 (OUTLIER) cc_final: -0.1921 (p0) REVERT: 4 527 ASN cc_start: 0.8221 (t0) cc_final: 0.7858 (t0) REVERT: 4 533 GLN cc_start: 0.6020 (OUTLIER) cc_final: 0.4649 (tm-30) REVERT: 4 615 ILE cc_start: 0.8954 (tt) cc_final: 0.8667 (mp) REVERT: 4 620 ASN cc_start: 0.5935 (p0) cc_final: 0.5605 (p0) REVERT: 4 713 ILE cc_start: 0.7621 (mt) cc_final: 0.7300 (mm) REVERT: 7 64 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8427 (pm20) REVERT: 7 79 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6270 (p0) REVERT: 7 200 PHE cc_start: 0.7623 (t80) cc_final: 0.7342 (t80) REVERT: 7 221 TYR cc_start: 0.7458 (m-80) cc_final: 0.7089 (m-10) REVERT: 7 242 ASP cc_start: 0.8049 (t70) cc_final: 0.7717 (t0) REVERT: 7 298 LEU cc_start: 0.7618 (tp) cc_final: 0.7326 (tt) REVERT: 7 304 ILE cc_start: 0.2501 (OUTLIER) cc_final: 0.1801 (tt) REVERT: 7 387 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8441 (pttm) REVERT: 7 465 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.6408 (tt0) REVERT: 7 522 GLN cc_start: 0.2387 (OUTLIER) cc_final: 0.1979 (tp-100) REVERT: 7 541 HIS cc_start: 0.6251 (m90) cc_final: 0.5379 (m90) REVERT: 7 559 MET cc_start: 0.6862 (mtp) cc_final: 0.6267 (mtp) REVERT: 7 561 ARG cc_start: 0.8056 (mtt90) cc_final: 0.7755 (mtp85) REVERT: 7 630 VAL cc_start: 0.8767 (t) cc_final: 0.8566 (p) REVERT: 7 639 MET cc_start: 0.7220 (tpp) cc_final: 0.6460 (tpp) REVERT: 6 69 LEU cc_start: 0.5867 (mp) cc_final: 0.5619 (mt) REVERT: 6 76 GLU cc_start: 0.3532 (mt-10) cc_final: 0.3127 (mp0) REVERT: 6 86 GLN cc_start: 0.9411 (tt0) cc_final: 0.9170 (tm-30) REVERT: 6 131 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6945 (tp) REVERT: 6 223 ARG cc_start: 0.6944 (mtt180) cc_final: 0.6341 (ptt-90) REVERT: 6 235 ARG cc_start: 0.7600 (mmt-90) cc_final: 0.7126 (mmt-90) REVERT: 6 355 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7576 (pm20) REVERT: 6 389 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6658 (m-30) REVERT: 6 404 PHE cc_start: 0.5840 (t80) cc_final: 0.5445 (t80) REVERT: 6 432 PHE cc_start: -0.0085 (OUTLIER) cc_final: -0.0326 (m-80) REVERT: 6 442 MET cc_start: 0.6171 (ttt) cc_final: 0.5111 (mmm) REVERT: 6 443 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7289 (pp) REVERT: 6 486 ASN cc_start: 0.7547 (p0) cc_final: 0.6779 (p0) REVERT: 6 506 LYS cc_start: 0.5455 (mtpt) cc_final: 0.5251 (mmtp) REVERT: 6 537 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7383 (t0) REVERT: 5 32 LYS cc_start: 0.7994 (mmmm) cc_final: 0.7527 (mmtm) REVERT: 5 37 PHE cc_start: 0.7209 (t80) cc_final: 0.6587 (t80) REVERT: 5 52 ASP cc_start: 0.9097 (m-30) cc_final: 0.8728 (p0) REVERT: 5 62 ARG cc_start: 0.7585 (mmt-90) cc_final: 0.7213 (ttm110) REVERT: 5 66 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8307 (pm20) REVERT: 5 69 MET cc_start: 0.2054 (ptt) cc_final: 0.1571 (mmm) REVERT: 5 216 CYS cc_start: 0.6715 (p) cc_final: 0.6441 (p) REVERT: 5 322 MET cc_start: 0.6314 (mtt) cc_final: 0.5909 (tpt) REVERT: 5 416 MET cc_start: 0.5639 (ppp) cc_final: 0.5130 (ppp) REVERT: 5 418 ASP cc_start: 0.5986 (OUTLIER) cc_final: 0.5761 (p0) REVERT: 5 426 MET cc_start: 0.4370 (ptm) cc_final: 0.3762 (ppp) REVERT: 5 459 MET cc_start: 0.5427 (mpp) cc_final: 0.5142 (ptt) REVERT: 5 474 THR cc_start: 0.7615 (m) cc_final: 0.7183 (p) REVERT: 5 515 PHE cc_start: 0.6154 (m-80) cc_final: 0.3484 (m-80) REVERT: 5 556 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7683 (t) REVERT: 5 612 LEU cc_start: 0.7831 (tt) cc_final: 0.7508 (tt) REVERT: 5 641 ARG cc_start: 0.8676 (mtt90) cc_final: 0.7509 (tmm-80) REVERT: A 20 LEU cc_start: 0.9163 (tt) cc_final: 0.8935 (tt) REVERT: A 77 CYS cc_start: 0.1151 (OUTLIER) cc_final: 0.0540 (t) REVERT: A 99 ASP cc_start: 0.6148 (t70) cc_final: 0.5796 (t0) REVERT: A 100 SER cc_start: 0.6360 (m) cc_final: 0.6049 (t) REVERT: A 229 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7232 (t0) REVERT: A 259 GLU cc_start: 0.9001 (tt0) cc_final: 0.8741 (tm-30) REVERT: A 276 ASN cc_start: 0.7836 (p0) cc_final: 0.6901 (t0) REVERT: A 331 MET cc_start: 0.8246 (ttp) cc_final: 0.8014 (tpt) REVERT: A 378 TYR cc_start: 0.8004 (m-10) cc_final: 0.7640 (m-10) REVERT: A 383 ARG cc_start: 0.7938 (mmt-90) cc_final: 0.7219 (mtp85) REVERT: A 396 ILE cc_start: 0.5058 (OUTLIER) cc_final: 0.4272 (mt) REVERT: A 418 SER cc_start: 0.7421 (OUTLIER) cc_final: 0.7158 (p) REVERT: A 568 ASP cc_start: 0.8846 (m-30) cc_final: 0.8129 (t0) REVERT: H 35 ARG cc_start: 0.9244 (mmp80) cc_final: 0.8640 (mmp80) REVERT: H 36 GLN cc_start: 0.9374 (tp-100) cc_final: 0.9055 (tm-30) REVERT: H 120 ASN cc_start: 0.7235 (OUTLIER) cc_final: 0.6836 (t0) REVERT: L 73 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8514 (mt-10) REVERT: L 109 ARG cc_start: 0.7481 (mmt180) cc_final: 0.6938 (ttt90) REVERT: M 59 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7919 (tt) REVERT: M 126 ARG cc_start: 0.7683 (tpt-90) cc_final: 0.7462 (tpt170) REVERT: M 169 GLU cc_start: 0.8144 (mp0) cc_final: 0.6796 (tp30) REVERT: N 30 MET cc_start: 0.3466 (mtt) cc_final: 0.3223 (ptp) REVERT: N 48 ASN cc_start: 0.6563 (p0) cc_final: 0.6241 (p0) REVERT: N 115 PHE cc_start: 0.7144 (t80) cc_final: 0.6845 (t80) REVERT: 2 206 ARG cc_start: 0.8100 (mtm180) cc_final: 0.7451 (mtm110) REVERT: 2 212 MET cc_start: 0.7557 (tpp) cc_final: 0.7020 (tpp) REVERT: 2 351 GLU cc_start: 0.5799 (pt0) cc_final: 0.5282 (pt0) REVERT: 2 422 THR cc_start: 0.4890 (OUTLIER) cc_final: 0.4072 (p) REVERT: 2 518 LEU cc_start: 0.3951 (OUTLIER) cc_final: 0.3706 (pp) REVERT: 2 572 ASP cc_start: 0.7669 (m-30) cc_final: 0.7331 (m-30) REVERT: 2 609 CYS cc_start: 0.2940 (OUTLIER) cc_final: 0.1332 (m) REVERT: 2 716 ASP cc_start: 0.7661 (m-30) cc_final: 0.7099 (t0) REVERT: 2 742 ARG cc_start: 0.9116 (mtt90) cc_final: 0.8892 (mtp180) REVERT: 2 745 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8925 (tm-30) REVERT: 2 797 LYS cc_start: 0.3376 (mttt) cc_final: 0.3173 (mttt) outliers start: 314 outliers final: 91 residues processed: 1354 average time/residue: 0.5442 time to fit residues: 1158.4872 Evaluate side-chains 853 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 733 time to evaluate : 4.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 408 optimal weight: 0.9990 chunk 366 optimal weight: 0.0980 chunk 203 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 195 optimal weight: 0.1980 chunk 379 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 230 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 439 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 194 GLN 3 199 GLN 3 381 GLN 3 546 HIS 4 204 HIS 4 223 GLN 4 228 GLN 4 386 GLN 4 441 HIS 4 494 HIS 4 507 HIS ** 4 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 595 GLN ** 4 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 45 GLN ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 536 HIS 6 181 ASN 6 198 GLN 6 364 GLN ** 6 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 550 ASN ** 5 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 456 HIS 5 537 HIS ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 GLN A 290 HIS A 296 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 HIS M 164 ASN N 69 GLN N 142 GLN N 180 HIS 2 211 ASN 2 227 HIS 2 352 GLN 2 364 GLN 2 450 GLN ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 668 HIS 2 758 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5840 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 39744 Z= 0.237 Angle : 0.867 11.438 53737 Z= 0.449 Chirality : 0.050 0.246 6083 Planarity : 0.007 0.087 6914 Dihedral : 12.602 176.994 5609 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.82 % Favored : 87.10 % Rotamer: Outliers : 0.38 % Allowed : 7.07 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.89 (0.10), residues: 4775 helix: -2.96 (0.11), residues: 1423 sheet: -3.42 (0.20), residues: 414 loop : -3.55 (0.10), residues: 2938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 7 519 HIS 0.010 0.001 HIS 6 584 PHE 0.040 0.002 PHE A 482 TYR 0.033 0.002 TYR 2 471 ARG 0.009 0.001 ARG 5 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 953 time to evaluate : 4.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3 130 LYS cc_start: 0.5105 (mtpt) cc_final: 0.4045 (mptt) REVERT: 3 230 ASP cc_start: 0.6081 (t0) cc_final: 0.5234 (t0) REVERT: 3 419 GLU cc_start: 0.7414 (tt0) cc_final: 0.7100 (tm-30) REVERT: 3 448 ASN cc_start: 0.6644 (t0) cc_final: 0.6356 (m-40) REVERT: 3 572 MET cc_start: 0.4621 (mmp) cc_final: 0.3437 (tpt) REVERT: 3 627 MET cc_start: 0.7397 (ptp) cc_final: 0.6682 (ptp) REVERT: 4 210 TYR cc_start: 0.6109 (m-80) cc_final: 0.5733 (m-80) REVERT: 4 224 ASP cc_start: 0.8489 (t0) cc_final: 0.7942 (t0) REVERT: 4 282 MET cc_start: 0.7929 (tpp) cc_final: 0.7635 (tpp) REVERT: 4 295 SER cc_start: 0.6002 (m) cc_final: 0.5787 (p) REVERT: 4 299 ILE cc_start: 0.8051 (mm) cc_final: 0.7759 (tp) REVERT: 4 306 PHE cc_start: 0.6099 (t80) cc_final: 0.5816 (t80) REVERT: 4 356 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7781 (ttmm) REVERT: 4 363 ASP cc_start: 0.7334 (m-30) cc_final: 0.7049 (t0) REVERT: 4 371 HIS cc_start: 0.5756 (m-70) cc_final: 0.5072 (m-70) REVERT: 4 378 HIS cc_start: 0.7238 (m-70) cc_final: 0.6533 (m-70) REVERT: 4 484 LEU cc_start: 0.6227 (mt) cc_final: 0.5660 (mt) REVERT: 4 758 LEU cc_start: 0.8022 (mp) cc_final: 0.7558 (tp) REVERT: 7 33 TYR cc_start: 0.6854 (t80) cc_final: 0.6640 (t80) REVERT: 7 174 LYS cc_start: 0.8905 (mmtm) cc_final: 0.8455 (mmmm) REVERT: 7 176 MET cc_start: 0.4330 (ttp) cc_final: 0.4008 (ttp) REVERT: 7 200 PHE cc_start: 0.7464 (t80) cc_final: 0.6961 (t80) REVERT: 7 221 TYR cc_start: 0.7747 (m-80) cc_final: 0.7208 (m-10) REVERT: 7 242 ASP cc_start: 0.8072 (t70) cc_final: 0.7820 (t0) REVERT: 7 293 LEU cc_start: 0.8472 (mm) cc_final: 0.8174 (mm) REVERT: 7 327 LEU cc_start: 0.8521 (tp) cc_final: 0.8286 (mt) REVERT: 7 349 ASP cc_start: 0.8273 (m-30) cc_final: 0.7980 (t0) REVERT: 7 365 ARG cc_start: 0.7046 (tmt170) cc_final: 0.6566 (tpt-90) REVERT: 7 369 MET cc_start: 0.5756 (tpt) cc_final: 0.3846 (mpp) REVERT: 7 559 MET cc_start: 0.6859 (mtp) cc_final: 0.6518 (mtp) REVERT: 7 561 ARG cc_start: 0.8289 (mtt90) cc_final: 0.7820 (mtp85) REVERT: 7 570 ASN cc_start: 0.5419 (m110) cc_final: 0.5060 (p0) REVERT: 7 591 GLU cc_start: 0.8399 (pt0) cc_final: 0.7934 (pm20) REVERT: 7 639 MET cc_start: 0.6419 (tpp) cc_final: 0.5626 (tpp) REVERT: 6 76 GLU cc_start: 0.3432 (mt-10) cc_final: 0.2907 (mp0) REVERT: 6 115 HIS cc_start: 0.8917 (m-70) cc_final: 0.8587 (m170) REVERT: 6 131 ILE cc_start: 0.8018 (pt) cc_final: 0.7801 (tp) REVERT: 6 186 MET cc_start: 0.2994 (tpt) cc_final: 0.2679 (tpt) REVERT: 6 223 ARG cc_start: 0.6731 (mtt180) cc_final: 0.6395 (ptt-90) REVERT: 6 404 PHE cc_start: 0.5849 (t80) cc_final: 0.5564 (t80) REVERT: 6 442 MET cc_start: 0.5997 (ttt) cc_final: 0.4913 (mmm) REVERT: 6 486 ASN cc_start: 0.7461 (p0) cc_final: 0.6454 (p0) REVERT: 6 585 MET cc_start: 0.7971 (mmm) cc_final: 0.7539 (mmm) REVERT: 5 32 LYS cc_start: 0.7737 (mmmm) cc_final: 0.7281 (mmtm) REVERT: 5 37 PHE cc_start: 0.7139 (t80) cc_final: 0.6709 (t80) REVERT: 5 41 PHE cc_start: 0.7021 (t80) cc_final: 0.6132 (t80) REVERT: 5 52 ASP cc_start: 0.9042 (m-30) cc_final: 0.8713 (p0) REVERT: 5 62 ARG cc_start: 0.7732 (mmt-90) cc_final: 0.7339 (ttp-110) REVERT: 5 66 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8474 (mm-30) REVERT: 5 223 LYS cc_start: 0.7466 (tptt) cc_final: 0.7117 (tptm) REVERT: 5 241 GLN cc_start: 0.6425 (tp40) cc_final: 0.5948 (tp40) REVERT: 5 260 ILE cc_start: 0.7926 (pt) cc_final: 0.7406 (pt) REVERT: 5 314 ASP cc_start: 0.7228 (t70) cc_final: 0.6996 (t70) REVERT: 5 322 MET cc_start: 0.5780 (mtt) cc_final: 0.5516 (tpt) REVERT: 5 327 ASP cc_start: 0.7810 (m-30) cc_final: 0.7519 (m-30) REVERT: 5 426 MET cc_start: 0.4068 (ptm) cc_final: 0.3842 (ppp) REVERT: 5 641 ARG cc_start: 0.8635 (mtt90) cc_final: 0.7585 (tmm-80) REVERT: A 8 ASN cc_start: 0.8782 (m-40) cc_final: 0.8479 (p0) REVERT: A 212 ARG cc_start: 0.5310 (OUTLIER) cc_final: 0.5073 (ttt180) REVERT: A 229 ASN cc_start: 0.8808 (m-40) cc_final: 0.8355 (t0) REVERT: A 267 ARG cc_start: 0.7306 (tpt90) cc_final: 0.6603 (mmp80) REVERT: A 275 GLN cc_start: 0.7586 (pm20) cc_final: 0.7169 (tp40) REVERT: A 276 ASN cc_start: 0.7655 (p0) cc_final: 0.6679 (t0) REVERT: A 281 SER cc_start: 0.5603 (m) cc_final: 0.4937 (p) REVERT: A 287 ASN cc_start: 0.6514 (t0) cc_final: 0.6003 (m-40) REVERT: A 349 LEU cc_start: 0.7957 (mp) cc_final: 0.7521 (mt) REVERT: A 368 ASP cc_start: 0.8827 (m-30) cc_final: 0.8453 (t0) REVERT: A 376 LEU cc_start: 0.4632 (tp) cc_final: 0.4413 (tp) REVERT: A 568 ASP cc_start: 0.8597 (m-30) cc_final: 0.7811 (t0) REVERT: H 35 ARG cc_start: 0.8947 (mmp80) cc_final: 0.8532 (mmp80) REVERT: H 120 ASN cc_start: 0.6961 (t0) cc_final: 0.6187 (t0) REVERT: H 145 ASN cc_start: 0.1574 (t0) cc_final: 0.1255 (m-40) REVERT: H 159 CYS cc_start: 0.7050 (m) cc_final: 0.6750 (m) REVERT: L 53 ARG cc_start: 0.8026 (tpp-160) cc_final: 0.7811 (tpp-160) REVERT: L 109 ARG cc_start: 0.7661 (mmt180) cc_final: 0.6331 (ttt90) REVERT: L 125 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8178 (mt-10) REVERT: M 58 TYR cc_start: 0.7457 (p90) cc_final: 0.7125 (p90) REVERT: M 123 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7650 (mp0) REVERT: M 127 GLN cc_start: 0.8142 (mm110) cc_final: 0.7919 (mm110) REVERT: M 169 GLU cc_start: 0.8375 (mp0) cc_final: 0.7198 (tp30) REVERT: N 48 ASN cc_start: 0.6480 (p0) cc_final: 0.6114 (p0) REVERT: N 78 ARG cc_start: 0.8819 (tpp-160) cc_final: 0.8468 (mmm160) REVERT: N 101 MET cc_start: 0.8407 (mmp) cc_final: 0.8075 (mmm) REVERT: N 113 GLU cc_start: 0.9130 (tt0) cc_final: 0.8845 (pt0) REVERT: 2 277 GLU cc_start: 0.7154 (mp0) cc_final: 0.6546 (mp0) REVERT: 2 294 LEU cc_start: 0.7396 (pt) cc_final: 0.6925 (pt) REVERT: 2 352 GLN cc_start: 0.6303 (mp10) cc_final: 0.5926 (mp10) REVERT: 2 435 LYS cc_start: 0.8606 (tmmt) cc_final: 0.8238 (tttm) REVERT: 2 527 ARG cc_start: 0.6028 (mmt180) cc_final: 0.5365 (mmm160) REVERT: 2 716 ASP cc_start: 0.7724 (m-30) cc_final: 0.7421 (t0) REVERT: 2 745 GLU cc_start: 0.9210 (tm-30) cc_final: 0.8653 (tm-30) REVERT: 2 788 MET cc_start: 0.8930 (pmm) cc_final: 0.8390 (mmt) outliers start: 16 outliers final: 4 residues processed: 967 average time/residue: 0.5193 time to fit residues: 797.2432 Evaluate side-chains 696 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 691 time to evaluate : 4.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 244 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 365 optimal weight: 3.9990 chunk 299 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 440 optimal weight: 2.9990 chunk 475 optimal weight: 1.9990 chunk 392 optimal weight: 0.6980 chunk 436 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 353 optimal weight: 0.0060 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 546 HIS ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS 4 326 ASN 4 485 GLN 4 500 GLN 4 625 GLN 4 656 GLN 7 69 ASN ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 67 GLN 6 285 ASN 6 320 GLN ** 6 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 513 GLN 6 533 ASN ** 6 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 592 HIS 6 645 ASN 5 537 HIS 5 563 HIS ** 5 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN A 264 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 HIS M 151 ASN M 164 ASN N 118 HIS N 162 ASN N 164 GLN 2 211 ASN 2 450 GLN ** 2 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 39744 Z= 0.216 Angle : 0.775 11.793 53737 Z= 0.399 Chirality : 0.047 0.243 6083 Planarity : 0.006 0.074 6914 Dihedral : 12.011 179.418 5609 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.21 % Favored : 86.70 % Rotamer: Outliers : 0.17 % Allowed : 5.53 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.10), residues: 4775 helix: -2.51 (0.12), residues: 1395 sheet: -2.94 (0.21), residues: 432 loop : -3.23 (0.10), residues: 2948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 46 HIS 0.010 0.001 HIS 5 563 PHE 0.037 0.002 PHE A 482 TYR 0.036 0.002 TYR 6 559 ARG 0.013 0.001 ARG 2 461 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 876 time to evaluate : 4.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3 36 MET cc_start: 0.7335 (tpt) cc_final: 0.7119 (mmm) REVERT: 3 79 GLU cc_start: 0.7844 (pp20) cc_final: 0.7269 (mt-10) REVERT: 3 130 LYS cc_start: 0.4834 (mtpt) cc_final: 0.3898 (mptt) REVERT: 3 215 ASP cc_start: 0.7634 (p0) cc_final: 0.7334 (p0) REVERT: 3 419 GLU cc_start: 0.7481 (tt0) cc_final: 0.7156 (tm-30) REVERT: 3 572 MET cc_start: 0.5252 (mmp) cc_final: 0.4848 (ttt) REVERT: 3 627 MET cc_start: 0.7794 (ptp) cc_final: 0.6541 (ptm) REVERT: 4 295 SER cc_start: 0.6131 (m) cc_final: 0.5754 (p) REVERT: 4 306 PHE cc_start: 0.6044 (t80) cc_final: 0.5843 (t80) REVERT: 4 356 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7774 (ttpt) REVERT: 4 363 ASP cc_start: 0.7489 (m-30) cc_final: 0.7263 (t0) REVERT: 4 371 HIS cc_start: 0.5969 (m-70) cc_final: 0.5179 (m-70) REVERT: 4 378 HIS cc_start: 0.6967 (m-70) cc_final: 0.6030 (m-70) REVERT: 4 380 ASP cc_start: 0.8325 (m-30) cc_final: 0.8086 (p0) REVERT: 4 421 VAL cc_start: 0.7346 (t) cc_final: 0.6949 (t) REVERT: 4 615 ILE cc_start: 0.8150 (pt) cc_final: 0.7814 (mp) REVERT: 4 698 GLU cc_start: 0.7068 (tt0) cc_final: 0.5925 (tt0) REVERT: 4 712 LEU cc_start: 0.8184 (tp) cc_final: 0.7926 (pp) REVERT: 4 758 LEU cc_start: 0.8275 (mp) cc_final: 0.7853 (tp) REVERT: 7 221 TYR cc_start: 0.7296 (m-80) cc_final: 0.7044 (m-10) REVERT: 7 242 ASP cc_start: 0.8293 (t70) cc_final: 0.8073 (t0) REVERT: 7 293 LEU cc_start: 0.8636 (mm) cc_final: 0.8391 (mm) REVERT: 7 327 LEU cc_start: 0.8650 (tp) cc_final: 0.8358 (mt) REVERT: 7 349 ASP cc_start: 0.8194 (m-30) cc_final: 0.7972 (t0) REVERT: 7 369 MET cc_start: 0.5941 (tpt) cc_final: 0.4175 (mpp) REVERT: 7 454 ASP cc_start: 0.6062 (m-30) cc_final: 0.5719 (m-30) REVERT: 7 515 PHE cc_start: 0.7764 (m-80) cc_final: 0.7260 (m-80) REVERT: 7 541 HIS cc_start: 0.7032 (m90) cc_final: 0.6271 (m90) REVERT: 7 559 MET cc_start: 0.6849 (mtp) cc_final: 0.6573 (mtp) REVERT: 7 561 ARG cc_start: 0.8277 (mtt90) cc_final: 0.7866 (mtp85) REVERT: 6 76 GLU cc_start: 0.3269 (mt-10) cc_final: 0.2798 (mp0) REVERT: 6 131 ILE cc_start: 0.8291 (pt) cc_final: 0.8019 (tp) REVERT: 6 186 MET cc_start: 0.3330 (tpt) cc_final: 0.3052 (tpt) REVERT: 6 404 PHE cc_start: 0.6067 (t80) cc_final: 0.5863 (t80) REVERT: 6 442 MET cc_start: 0.5666 (ttt) cc_final: 0.4719 (mmm) REVERT: 6 486 ASN cc_start: 0.7730 (p0) cc_final: 0.6836 (p0) REVERT: 6 503 ASP cc_start: 0.6533 (t70) cc_final: 0.6259 (t0) REVERT: 6 585 MET cc_start: 0.8370 (mmm) cc_final: 0.7707 (mmm) REVERT: 6 625 LYS cc_start: 0.5722 (mtpp) cc_final: 0.5469 (tttt) REVERT: 6 638 LYS cc_start: 0.9029 (ptmt) cc_final: 0.8565 (ptpp) REVERT: 5 32 LYS cc_start: 0.7646 (mmmm) cc_final: 0.7339 (mptt) REVERT: 5 50 TYR cc_start: 0.7205 (m-10) cc_final: 0.6904 (m-10) REVERT: 5 52 ASP cc_start: 0.9051 (m-30) cc_final: 0.8698 (p0) REVERT: 5 62 ARG cc_start: 0.7647 (mmt-90) cc_final: 0.7325 (mmt-90) REVERT: 5 118 ASP cc_start: 0.7546 (m-30) cc_final: 0.7331 (m-30) REVERT: 5 246 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7288 (tpt90) REVERT: 5 260 ILE cc_start: 0.8078 (pt) cc_final: 0.7668 (pt) REVERT: 5 322 MET cc_start: 0.5882 (mtt) cc_final: 0.5597 (tpt) REVERT: 5 426 MET cc_start: 0.4147 (ptm) cc_final: 0.3945 (ppp) REVERT: 5 459 MET cc_start: 0.7720 (ppp) cc_final: 0.7369 (ppp) REVERT: 5 561 TYR cc_start: 0.8093 (t80) cc_final: 0.7790 (t80) REVERT: 5 641 ARG cc_start: 0.8782 (mtt90) cc_final: 0.7671 (tmm-80) REVERT: A 8 ASN cc_start: 0.8837 (m-40) cc_final: 0.8478 (p0) REVERT: A 9 ASP cc_start: 0.8681 (p0) cc_final: 0.7975 (p0) REVERT: A 10 PHE cc_start: 0.9048 (m-10) cc_final: 0.8678 (m-10) REVERT: A 275 GLN cc_start: 0.7591 (pm20) cc_final: 0.7354 (pm20) REVERT: A 276 ASN cc_start: 0.7477 (p0) cc_final: 0.6521 (t0) REVERT: A 368 ASP cc_start: 0.8873 (m-30) cc_final: 0.8350 (t0) REVERT: A 376 LEU cc_start: 0.5101 (tp) cc_final: 0.4851 (tp) REVERT: A 514 CYS cc_start: 0.5122 (m) cc_final: 0.4125 (t) REVERT: A 568 ASP cc_start: 0.8680 (m-30) cc_final: 0.7891 (t0) REVERT: H 145 ASN cc_start: 0.0992 (t0) cc_final: 0.0682 (m-40) REVERT: L 30 TYR cc_start: 0.7144 (t80) cc_final: 0.6670 (t80) REVERT: L 53 ARG cc_start: 0.8075 (tpp-160) cc_final: 0.7847 (tpp-160) REVERT: L 109 ARG cc_start: 0.7568 (mmt180) cc_final: 0.6676 (ttt90) REVERT: M 34 MET cc_start: 0.7753 (tmm) cc_final: 0.7364 (tmm) REVERT: M 58 TYR cc_start: 0.7421 (p90) cc_final: 0.6992 (p90) REVERT: M 107 TYR cc_start: 0.6999 (t80) cc_final: 0.6658 (t80) REVERT: M 123 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7759 (mm-30) REVERT: M 127 GLN cc_start: 0.8193 (mm110) cc_final: 0.7959 (mm110) REVERT: M 166 GLN cc_start: 0.9037 (pt0) cc_final: 0.8602 (mm-40) REVERT: M 169 GLU cc_start: 0.8436 (mp0) cc_final: 0.7656 (tp30) REVERT: N 78 ARG cc_start: 0.8926 (tpp-160) cc_final: 0.8598 (mmm160) REVERT: N 95 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8437 (mt-10) REVERT: N 96 ARG cc_start: 0.8270 (mtp-110) cc_final: 0.7563 (ttm170) REVERT: N 101 MET cc_start: 0.8260 (mmp) cc_final: 0.8056 (mmm) REVERT: N 110 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8288 (tm-30) REVERT: 2 210 GLN cc_start: 0.8065 (mp10) cc_final: 0.7704 (tp-100) REVERT: 2 227 HIS cc_start: 0.7251 (t-170) cc_final: 0.6918 (t-170) REVERT: 2 277 GLU cc_start: 0.6830 (mp0) cc_final: 0.6145 (mp0) REVERT: 2 294 LEU cc_start: 0.7727 (pt) cc_final: 0.7303 (pt) REVERT: 2 348 ILE cc_start: 0.8085 (pt) cc_final: 0.7733 (pt) REVERT: 2 435 LYS cc_start: 0.8828 (tmmt) cc_final: 0.8575 (tttm) REVERT: 2 527 ARG cc_start: 0.5898 (mmt180) cc_final: 0.5095 (mmm160) REVERT: 2 624 PRO cc_start: 0.6971 (Cg_endo) cc_final: 0.6514 (Cg_exo) REVERT: 2 716 ASP cc_start: 0.7845 (m-30) cc_final: 0.7572 (t0) REVERT: 2 745 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8795 (tm-30) REVERT: 2 788 MET cc_start: 0.8983 (pmm) cc_final: 0.8650 (mmt) outliers start: 7 outliers final: 3 residues processed: 881 average time/residue: 0.5170 time to fit residues: 727.5124 Evaluate side-chains 690 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 687 time to evaluate : 4.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 435 optimal weight: 0.1980 chunk 331 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 295 optimal weight: 4.9990 chunk 441 optimal weight: 4.9990 chunk 467 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 418 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS 4 494 HIS ** 4 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 238 GLN 7 270 HIS ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 465 GLN ** 7 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 341 ASN ** 6 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 499 ASN ** 6 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 456 HIS 5 563 HIS ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 HIS A 431 GLN H 36 GLN ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 211 ASN ** 2 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 39744 Z= 0.354 Angle : 0.902 11.683 53737 Z= 0.467 Chirality : 0.051 0.271 6083 Planarity : 0.007 0.087 6914 Dihedral : 12.087 179.093 5609 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 26.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 15.04 % Favored : 84.86 % Rotamer: Outliers : 0.28 % Allowed : 6.69 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.10), residues: 4775 helix: -2.50 (0.12), residues: 1401 sheet: -3.10 (0.21), residues: 435 loop : -3.19 (0.10), residues: 2939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP N 46 HIS 0.013 0.002 HIS 5 456 PHE 0.034 0.003 PHE 3 406 TYR 0.049 0.003 TYR 7 33 ARG 0.013 0.001 ARG 6 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 851 time to evaluate : 4.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3 44 LEU cc_start: 0.8023 (mt) cc_final: 0.7814 (mp) REVERT: 3 130 LYS cc_start: 0.5554 (mtpt) cc_final: 0.4475 (mptt) REVERT: 3 197 THR cc_start: 0.3286 (p) cc_final: 0.2869 (p) REVERT: 3 227 LYS cc_start: 0.5552 (ptpp) cc_final: 0.5226 (pttm) REVERT: 3 405 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7504 (mp0) REVERT: 3 419 GLU cc_start: 0.7474 (tt0) cc_final: 0.7133 (tm-30) REVERT: 3 572 MET cc_start: 0.5820 (mmp) cc_final: 0.5430 (ttt) REVERT: 3 628 SER cc_start: 0.6293 (m) cc_final: 0.5996 (m) REVERT: 4 226 TYR cc_start: 0.9153 (t80) cc_final: 0.8948 (t80) REVERT: 4 295 SER cc_start: 0.6628 (m) cc_final: 0.6347 (p) REVERT: 4 306 PHE cc_start: 0.6292 (t80) cc_final: 0.6065 (t80) REVERT: 4 356 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7897 (ttmm) REVERT: 4 363 ASP cc_start: 0.7551 (m-30) cc_final: 0.7273 (t0) REVERT: 4 371 HIS cc_start: 0.6203 (m-70) cc_final: 0.5542 (m-70) REVERT: 4 520 GLN cc_start: 0.8373 (tt0) cc_final: 0.8016 (mt0) REVERT: 4 758 LEU cc_start: 0.8417 (mp) cc_final: 0.8169 (tp) REVERT: 7 174 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8482 (mmtp) REVERT: 7 221 TYR cc_start: 0.7129 (m-80) cc_final: 0.6873 (m-10) REVERT: 7 241 SER cc_start: 0.7078 (p) cc_final: 0.6220 (m) REVERT: 7 327 LEU cc_start: 0.8575 (tp) cc_final: 0.8311 (mt) REVERT: 7 369 MET cc_start: 0.5354 (tpt) cc_final: 0.4542 (mpp) REVERT: 7 389 GLN cc_start: 0.8032 (pp30) cc_final: 0.7773 (pp30) REVERT: 7 559 MET cc_start: 0.7364 (mtp) cc_final: 0.6835 (mtp) REVERT: 7 561 ARG cc_start: 0.8241 (mtt90) cc_final: 0.7623 (mtp85) REVERT: 6 76 GLU cc_start: 0.3832 (mt-10) cc_final: 0.3421 (mp0) REVERT: 6 131 ILE cc_start: 0.8073 (pt) cc_final: 0.7819 (tp) REVERT: 6 186 MET cc_start: 0.4107 (tpt) cc_final: 0.3873 (tpt) REVERT: 6 223 ARG cc_start: 0.8094 (mtt180) cc_final: 0.6115 (ptt90) REVERT: 6 442 MET cc_start: 0.5988 (ttt) cc_final: 0.5306 (ttt) REVERT: 6 503 ASP cc_start: 0.6555 (t70) cc_final: 0.6195 (t0) REVERT: 6 520 SER cc_start: 0.7305 (t) cc_final: 0.6956 (p) REVERT: 6 585 MET cc_start: 0.8206 (mmm) cc_final: 0.7573 (mmm) REVERT: 6 588 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8249 (mp0) REVERT: 6 594 ARG cc_start: 0.6149 (ptm160) cc_final: 0.5674 (ptm160) REVERT: 6 638 LYS cc_start: 0.8919 (ptmt) cc_final: 0.8560 (pttm) REVERT: 5 32 LYS cc_start: 0.7741 (mmmm) cc_final: 0.7262 (mmtm) REVERT: 5 52 ASP cc_start: 0.9136 (m-30) cc_final: 0.8896 (p0) REVERT: 5 62 ARG cc_start: 0.7987 (mmt-90) cc_final: 0.7683 (mmt-90) REVERT: 5 66 GLU cc_start: 0.9143 (tt0) cc_final: 0.8471 (tp30) REVERT: 5 100 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8952 (mm-30) REVERT: 5 116 MET cc_start: 0.5743 (ttp) cc_final: 0.5524 (tmm) REVERT: 5 118 ASP cc_start: 0.7973 (m-30) cc_final: 0.7557 (m-30) REVERT: 5 156 ILE cc_start: 0.8979 (tt) cc_final: 0.8625 (mm) REVERT: 5 223 LYS cc_start: 0.7711 (tptm) cc_final: 0.7462 (tptm) REVERT: 5 246 ARG cc_start: 0.8514 (mtt90) cc_final: 0.7970 (tpt90) REVERT: 5 314 ASP cc_start: 0.7222 (t70) cc_final: 0.6994 (t70) REVERT: 5 362 LEU cc_start: 0.8623 (mp) cc_final: 0.8337 (pt) REVERT: 5 426 MET cc_start: 0.4104 (ptm) cc_final: 0.3897 (ppp) REVERT: 5 641 ARG cc_start: 0.8836 (mtt90) cc_final: 0.7659 (tmm-80) REVERT: A 8 ASN cc_start: 0.8935 (m-40) cc_final: 0.8596 (p0) REVERT: A 9 ASP cc_start: 0.8775 (p0) cc_final: 0.8269 (p0) REVERT: A 10 PHE cc_start: 0.8974 (m-10) cc_final: 0.8657 (m-10) REVERT: A 13 GLN cc_start: 0.9230 (tt0) cc_final: 0.8852 (tm-30) REVERT: A 229 ASN cc_start: 0.9065 (m-40) cc_final: 0.8794 (m110) REVERT: A 259 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8642 (pt0) REVERT: A 276 ASN cc_start: 0.7850 (p0) cc_final: 0.7047 (t0) REVERT: A 368 ASP cc_start: 0.9099 (m-30) cc_final: 0.8467 (t0) REVERT: A 383 ARG cc_start: 0.7581 (mmt-90) cc_final: 0.6997 (mpt180) REVERT: A 568 ASP cc_start: 0.8958 (m-30) cc_final: 0.8040 (t0) REVERT: H 75 GLN cc_start: 0.9258 (mm110) cc_final: 0.8975 (mm110) REVERT: H 160 MET cc_start: 0.4349 (mtm) cc_final: 0.3188 (tpp) REVERT: L 43 PHE cc_start: 0.7579 (p90) cc_final: 0.6843 (p90) REVERT: L 109 ARG cc_start: 0.7804 (mmt180) cc_final: 0.6725 (ttm170) REVERT: L 125 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8384 (mp0) REVERT: M 34 MET cc_start: 0.7734 (tmm) cc_final: 0.7371 (tmm) REVERT: M 107 TYR cc_start: 0.7313 (t80) cc_final: 0.7006 (t80) REVERT: M 123 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8115 (tp30) REVERT: M 126 ARG cc_start: 0.8437 (tpt-90) cc_final: 0.6815 (tpt90) REVERT: M 127 GLN cc_start: 0.8543 (mm110) cc_final: 0.8275 (mm110) REVERT: M 166 GLN cc_start: 0.9049 (pt0) cc_final: 0.8623 (mm-40) REVERT: M 169 GLU cc_start: 0.8335 (mp0) cc_final: 0.7473 (tp30) REVERT: N 94 LEU cc_start: 0.9051 (tp) cc_final: 0.8612 (tp) REVERT: N 98 ARG cc_start: 0.9160 (mtm180) cc_final: 0.8802 (ptm160) REVERT: 2 212 MET cc_start: 0.8212 (mmp) cc_final: 0.7878 (mmp) REVERT: 2 294 LEU cc_start: 0.8054 (pt) cc_final: 0.7540 (pt) REVERT: 2 348 ILE cc_start: 0.8165 (pt) cc_final: 0.7778 (pt) REVERT: 2 352 GLN cc_start: 0.6656 (mp10) cc_final: 0.6451 (mp10) REVERT: 2 398 GLU cc_start: 0.7976 (tp30) cc_final: 0.7452 (tm-30) REVERT: 2 527 ARG cc_start: 0.5856 (mmt180) cc_final: 0.5139 (mmm160) REVERT: 2 624 PRO cc_start: 0.7358 (Cg_endo) cc_final: 0.6813 (Cg_exo) REVERT: 2 716 ASP cc_start: 0.8378 (m-30) cc_final: 0.8132 (t70) REVERT: 2 788 MET cc_start: 0.9041 (pmm) cc_final: 0.8719 (mmt) outliers start: 12 outliers final: 5 residues processed: 862 average time/residue: 0.5535 time to fit residues: 772.3670 Evaluate side-chains 674 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 669 time to evaluate : 4.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 389 optimal weight: 0.1980 chunk 265 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 348 optimal weight: 4.9990 chunk 193 optimal weight: 8.9990 chunk 399 optimal weight: 6.9990 chunk 323 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 238 optimal weight: 0.6980 chunk 419 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS ** 4 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 465 GLN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN H 199 HIS M 164 ASN ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 223 ASN 2 211 ASN 2 450 GLN ** 2 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 606 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39744 Z= 0.204 Angle : 0.751 11.279 53737 Z= 0.384 Chirality : 0.046 0.207 6083 Planarity : 0.005 0.060 6914 Dihedral : 11.631 178.217 5609 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.59 % Favored : 87.35 % Rotamer: Outliers : 0.14 % Allowed : 4.15 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.11), residues: 4775 helix: -2.29 (0.12), residues: 1420 sheet: -2.84 (0.21), residues: 452 loop : -3.02 (0.10), residues: 2903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 46 HIS 0.007 0.001 HIS 7 459 PHE 0.036 0.002 PHE 7 77 TYR 0.023 0.002 TYR 3 16 ARG 0.009 0.001 ARG L 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 837 time to evaluate : 4.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3 79 GLU cc_start: 0.8112 (pp20) cc_final: 0.7166 (mt-10) REVERT: 3 130 LYS cc_start: 0.5086 (mtpt) cc_final: 0.4091 (mptt) REVERT: 3 197 THR cc_start: 0.2870 (p) cc_final: 0.2417 (p) REVERT: 3 227 LYS cc_start: 0.5568 (ptpp) cc_final: 0.5218 (pttm) REVERT: 3 405 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7304 (mp0) REVERT: 3 423 GLN cc_start: 0.7375 (tp40) cc_final: 0.6262 (pt0) REVERT: 3 462 GLU cc_start: 0.5657 (mm-30) cc_final: 0.5364 (mm-30) REVERT: 3 572 MET cc_start: 0.5690 (mmp) cc_final: 0.5476 (ttt) REVERT: 3 628 SER cc_start: 0.6594 (m) cc_final: 0.6202 (p) REVERT: 4 282 MET cc_start: 0.8497 (tpp) cc_final: 0.8081 (tpp) REVERT: 4 306 PHE cc_start: 0.6192 (t80) cc_final: 0.5960 (t80) REVERT: 4 356 LYS cc_start: 0.8142 (ttmm) cc_final: 0.7597 (ttpt) REVERT: 4 371 HIS cc_start: 0.5858 (m-70) cc_final: 0.5231 (m-70) REVERT: 4 520 GLN cc_start: 0.8328 (tt0) cc_final: 0.8096 (mt0) REVERT: 4 698 GLU cc_start: 0.7127 (tt0) cc_final: 0.6346 (tt0) REVERT: 4 758 LEU cc_start: 0.8503 (mp) cc_final: 0.8149 (tp) REVERT: 7 174 LYS cc_start: 0.8988 (mmtm) cc_final: 0.8662 (mmtp) REVERT: 7 242 ASP cc_start: 0.8043 (t0) cc_final: 0.7705 (t0) REVERT: 7 261 VAL cc_start: 0.7979 (t) cc_final: 0.7292 (t) REVERT: 7 327 LEU cc_start: 0.8757 (tp) cc_final: 0.8470 (mt) REVERT: 7 363 ASP cc_start: 0.7164 (m-30) cc_final: 0.6657 (m-30) REVERT: 7 369 MET cc_start: 0.5662 (tpt) cc_final: 0.4937 (mpp) REVERT: 7 389 GLN cc_start: 0.7740 (pp30) cc_final: 0.7368 (pp30) REVERT: 7 559 MET cc_start: 0.7310 (mtp) cc_final: 0.6822 (mtp) REVERT: 7 561 ARG cc_start: 0.8292 (mtt90) cc_final: 0.7634 (mtp85) REVERT: 7 572 THR cc_start: 0.6021 (t) cc_final: 0.5725 (m) REVERT: 6 76 GLU cc_start: 0.3432 (mt-10) cc_final: 0.3194 (mp0) REVERT: 6 131 ILE cc_start: 0.8312 (pt) cc_final: 0.8050 (tp) REVERT: 6 186 MET cc_start: 0.4041 (tpt) cc_final: 0.3408 (tpt) REVERT: 6 223 ARG cc_start: 0.7927 (mtt180) cc_final: 0.5892 (ptt-90) REVERT: 6 288 MET cc_start: 0.7623 (tpp) cc_final: 0.6040 (tpp) REVERT: 6 442 MET cc_start: 0.5964 (ttt) cc_final: 0.5296 (ttt) REVERT: 6 469 MET cc_start: 0.4629 (tpp) cc_final: 0.4270 (pmm) REVERT: 6 503 ASP cc_start: 0.6350 (t70) cc_final: 0.6023 (t0) REVERT: 6 588 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8495 (tm-30) REVERT: 6 592 HIS cc_start: 0.8064 (m90) cc_final: 0.7313 (t-170) REVERT: 5 32 LYS cc_start: 0.7571 (mmmm) cc_final: 0.7161 (mptt) REVERT: 5 52 ASP cc_start: 0.9037 (m-30) cc_final: 0.8831 (p0) REVERT: 5 62 ARG cc_start: 0.7949 (mmt-90) cc_final: 0.7091 (ttm-80) REVERT: 5 66 GLU cc_start: 0.9112 (tt0) cc_final: 0.8556 (tm-30) REVERT: 5 171 SER cc_start: 0.7637 (m) cc_final: 0.7151 (p) REVERT: 5 223 LYS cc_start: 0.7523 (tptm) cc_final: 0.7253 (tptp) REVERT: 5 246 ARG cc_start: 0.8386 (mtt90) cc_final: 0.7994 (tpt90) REVERT: 5 362 LEU cc_start: 0.8582 (mp) cc_final: 0.8232 (pt) REVERT: 5 416 MET cc_start: 0.5687 (ppp) cc_final: 0.4884 (ptt) REVERT: 5 426 MET cc_start: 0.4283 (ptm) cc_final: 0.4073 (ppp) REVERT: 5 456 HIS cc_start: 0.8132 (t70) cc_final: 0.7816 (t-170) REVERT: 5 641 ARG cc_start: 0.8869 (mtt90) cc_final: 0.7781 (tmm-80) REVERT: A 8 ASN cc_start: 0.8821 (m-40) cc_final: 0.8531 (p0) REVERT: A 13 GLN cc_start: 0.9169 (tt0) cc_final: 0.8842 (tm-30) REVERT: A 116 CYS cc_start: 0.6525 (t) cc_final: 0.6094 (p) REVERT: A 229 ASN cc_start: 0.8983 (m-40) cc_final: 0.8646 (m110) REVERT: A 243 GLN cc_start: 0.5734 (mm-40) cc_final: 0.4979 (tm-30) REVERT: A 259 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8553 (pt0) REVERT: A 276 ASN cc_start: 0.7815 (p0) cc_final: 0.7003 (t0) REVERT: A 347 LEU cc_start: 0.9121 (pp) cc_final: 0.8304 (tp) REVERT: A 368 ASP cc_start: 0.9047 (m-30) cc_final: 0.8469 (t0) REVERT: A 383 ARG cc_start: 0.7568 (mmt-90) cc_final: 0.7143 (mpt180) REVERT: A 424 LEU cc_start: 0.8912 (pp) cc_final: 0.8682 (pp) REVERT: A 514 CYS cc_start: 0.5954 (m) cc_final: 0.5434 (t) REVERT: A 568 ASP cc_start: 0.8932 (m-30) cc_final: 0.7994 (t0) REVERT: H 35 ARG cc_start: 0.9022 (mmp80) cc_final: 0.8384 (ttp80) REVERT: H 75 GLN cc_start: 0.9072 (mm110) cc_final: 0.8729 (mm110) REVERT: H 160 MET cc_start: 0.4292 (mtm) cc_final: 0.3244 (tpp) REVERT: L 14 MET cc_start: 0.3907 (mtp) cc_final: 0.3656 (mtp) REVERT: L 54 LYS cc_start: 0.8711 (ptmt) cc_final: 0.8418 (mtmm) REVERT: L 109 ARG cc_start: 0.7805 (mmt180) cc_final: 0.6641 (ttm170) REVERT: L 125 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8257 (mp0) REVERT: M 68 TYR cc_start: 0.7806 (m-10) cc_final: 0.7541 (m-10) REVERT: M 77 TYR cc_start: 0.7665 (m-10) cc_final: 0.6592 (m-80) REVERT: M 107 TYR cc_start: 0.7098 (t80) cc_final: 0.6777 (t80) REVERT: M 123 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8174 (tp30) REVERT: M 126 ARG cc_start: 0.8268 (tpt-90) cc_final: 0.6661 (tpt90) REVERT: M 127 GLN cc_start: 0.8351 (mm110) cc_final: 0.8146 (mm110) REVERT: M 132 LEU cc_start: 0.5975 (mp) cc_final: 0.4763 (pp) REVERT: M 166 GLN cc_start: 0.8971 (pt0) cc_final: 0.8543 (mm-40) REVERT: M 169 GLU cc_start: 0.8353 (mp0) cc_final: 0.7601 (tp30) REVERT: N 94 LEU cc_start: 0.9024 (tp) cc_final: 0.8824 (tp) REVERT: N 95 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8579 (mt-10) REVERT: 2 212 MET cc_start: 0.7823 (mmp) cc_final: 0.7523 (mmp) REVERT: 2 294 LEU cc_start: 0.7911 (pt) cc_final: 0.7458 (pt) REVERT: 2 348 ILE cc_start: 0.8097 (pt) cc_final: 0.7694 (pt) REVERT: 2 527 ARG cc_start: 0.5635 (mmt180) cc_final: 0.5005 (mmm160) REVERT: 2 624 PRO cc_start: 0.7029 (Cg_endo) cc_final: 0.6361 (Cg_exo) REVERT: 2 630 GLU cc_start: 0.7916 (mp0) cc_final: 0.7436 (mp0) REVERT: 2 716 ASP cc_start: 0.8294 (m-30) cc_final: 0.8074 (t70) REVERT: 2 743 HIS cc_start: 0.8289 (t-90) cc_final: 0.8070 (t-170) REVERT: 2 788 MET cc_start: 0.9099 (pmm) cc_final: 0.8775 (mmt) REVERT: 2 791 MET cc_start: 0.6030 (mmm) cc_final: 0.5693 (mmm) outliers start: 6 outliers final: 4 residues processed: 841 average time/residue: 0.5136 time to fit residues: 695.2448 Evaluate side-chains 681 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 677 time to evaluate : 4.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 157 optimal weight: 0.3980 chunk 421 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 274 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 468 optimal weight: 0.4980 chunk 388 optimal weight: 8.9990 chunk 216 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 154 optimal weight: 0.0770 chunk 245 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS ** 4 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 557 ASN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 466 HIS 6 584 HIS ** 6 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 645 ASN ** 5 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 563 HIS ** 5 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN H 199 HIS M 164 ASN ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 GLN ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 211 ASN ** 2 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39744 Z= 0.179 Angle : 0.714 11.914 53737 Z= 0.361 Chirality : 0.045 0.233 6083 Planarity : 0.005 0.061 6914 Dihedral : 11.116 176.521 5609 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.23 % Favored : 87.73 % Rotamer: Outliers : 0.14 % Allowed : 2.75 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.79 (0.11), residues: 4775 helix: -2.05 (0.12), residues: 1430 sheet: -2.62 (0.22), residues: 447 loop : -2.88 (0.11), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 297 HIS 0.010 0.001 HIS H 199 PHE 0.022 0.002 PHE N 115 TYR 0.018 0.002 TYR 5 48 ARG 0.016 0.001 ARG 3 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 824 time to evaluate : 4.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 125 GLU cc_start: 0.8728 (pm20) cc_final: 0.8410 (pm20) REVERT: 3 130 LYS cc_start: 0.4781 (mtpt) cc_final: 0.4009 (mptt) REVERT: 3 387 ARG cc_start: 0.6637 (ptm-80) cc_final: 0.6327 (ptm-80) REVERT: 3 405 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7248 (mp0) REVERT: 3 423 GLN cc_start: 0.7327 (tp40) cc_final: 0.6288 (pt0) REVERT: 3 557 LEU cc_start: 0.7063 (tt) cc_final: 0.6525 (mp) REVERT: 3 628 SER cc_start: 0.6839 (m) cc_final: 0.6204 (p) REVERT: 4 226 TYR cc_start: 0.9074 (t80) cc_final: 0.8871 (t80) REVERT: 4 247 MET cc_start: 0.8275 (ttp) cc_final: 0.7324 (tpp) REVERT: 4 282 MET cc_start: 0.8476 (tpp) cc_final: 0.8020 (tpp) REVERT: 4 345 ASN cc_start: 0.8408 (m110) cc_final: 0.8151 (t0) REVERT: 4 356 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7907 (ttmm) REVERT: 4 371 HIS cc_start: 0.6031 (m-70) cc_final: 0.5491 (m-70) REVERT: 4 520 GLN cc_start: 0.8269 (tt0) cc_final: 0.8037 (mt0) REVERT: 4 577 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7677 (mm-30) REVERT: 4 578 PHE cc_start: 0.7250 (t80) cc_final: 0.6741 (t80) REVERT: 4 586 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7775 (ttm170) REVERT: 4 591 GLU cc_start: 0.6482 (tp30) cc_final: 0.6158 (tp30) REVERT: 4 707 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6796 (pm20) REVERT: 4 758 LEU cc_start: 0.8446 (mp) cc_final: 0.8046 (tp) REVERT: 7 242 ASP cc_start: 0.8031 (t0) cc_final: 0.7651 (t0) REVERT: 7 327 LEU cc_start: 0.8654 (tp) cc_final: 0.8400 (mt) REVERT: 7 365 ARG cc_start: 0.6918 (tmt170) cc_final: 0.6714 (tmt170) REVERT: 7 369 MET cc_start: 0.6158 (tpt) cc_final: 0.5456 (mpp) REVERT: 7 460 GLU cc_start: 0.7396 (tt0) cc_final: 0.7147 (tt0) REVERT: 7 559 MET cc_start: 0.7300 (mtp) cc_final: 0.6915 (mtp) REVERT: 6 131 ILE cc_start: 0.8443 (pt) cc_final: 0.8152 (tp) REVERT: 6 186 MET cc_start: 0.4175 (tpt) cc_final: 0.3846 (tpt) REVERT: 6 223 ARG cc_start: 0.7890 (mtt180) cc_final: 0.5712 (ptt-90) REVERT: 6 442 MET cc_start: 0.5803 (ttt) cc_final: 0.5108 (ttt) REVERT: 6 469 MET cc_start: 0.5375 (tpp) cc_final: 0.4239 (pmm) REVERT: 6 503 ASP cc_start: 0.6293 (t70) cc_final: 0.5939 (t0) REVERT: 6 588 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8240 (tm-30) REVERT: 5 32 LYS cc_start: 0.7423 (mmmm) cc_final: 0.7002 (mptt) REVERT: 5 62 ARG cc_start: 0.7922 (mmt-90) cc_final: 0.7059 (ttm-80) REVERT: 5 171 SER cc_start: 0.7690 (m) cc_final: 0.7163 (p) REVERT: 5 223 LYS cc_start: 0.7465 (tptm) cc_final: 0.7227 (tptp) REVERT: 5 246 ARG cc_start: 0.8277 (mtt90) cc_final: 0.7964 (tpt90) REVERT: 5 456 HIS cc_start: 0.8136 (t70) cc_final: 0.7847 (t-170) REVERT: 5 474 THR cc_start: 0.7845 (m) cc_final: 0.7387 (p) REVERT: 5 641 ARG cc_start: 0.8923 (mtt90) cc_final: 0.7776 (tmm-80) REVERT: A 8 ASN cc_start: 0.8819 (m-40) cc_final: 0.8558 (p0) REVERT: A 9 ASP cc_start: 0.8709 (p0) cc_final: 0.8335 (p0) REVERT: A 53 MET cc_start: 0.8488 (tpt) cc_final: 0.8177 (tpt) REVERT: A 229 ASN cc_start: 0.9040 (m-40) cc_final: 0.8690 (m110) REVERT: A 230 MET cc_start: 0.8131 (mtp) cc_final: 0.7842 (mtp) REVERT: A 243 GLN cc_start: 0.5976 (mm-40) cc_final: 0.5308 (tm-30) REVERT: A 259 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8082 (mm-30) REVERT: A 276 ASN cc_start: 0.8016 (p0) cc_final: 0.7213 (t0) REVERT: A 347 LEU cc_start: 0.9133 (pp) cc_final: 0.8372 (tp) REVERT: A 368 ASP cc_start: 0.8896 (m-30) cc_final: 0.8052 (t0) REVERT: A 376 LEU cc_start: 0.5924 (tp) cc_final: 0.5527 (tp) REVERT: A 383 ARG cc_start: 0.7386 (mmt-90) cc_final: 0.7048 (mpt180) REVERT: A 440 PHE cc_start: 0.6652 (p90) cc_final: 0.6198 (p90) REVERT: A 514 CYS cc_start: 0.5981 (m) cc_final: 0.5453 (t) REVERT: A 568 ASP cc_start: 0.8947 (m-30) cc_final: 0.8011 (t0) REVERT: H 35 ARG cc_start: 0.9067 (mmp80) cc_final: 0.8387 (ttp80) REVERT: H 75 GLN cc_start: 0.8963 (mm110) cc_final: 0.8642 (mm110) REVERT: H 160 MET cc_start: 0.4128 (mtm) cc_final: 0.3164 (tpp) REVERT: L 70 ILE cc_start: 0.9136 (mt) cc_final: 0.8800 (mt) REVERT: L 109 ARG cc_start: 0.7781 (mmt180) cc_final: 0.6718 (ttt180) REVERT: L 112 GLU cc_start: 0.8339 (mp0) cc_final: 0.6915 (mp0) REVERT: L 125 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8261 (mp0) REVERT: M 58 TYR cc_start: 0.7412 (p90) cc_final: 0.7170 (p90) REVERT: M 107 TYR cc_start: 0.6885 (t80) cc_final: 0.6631 (t80) REVERT: M 123 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7798 (mm-30) REVERT: M 126 ARG cc_start: 0.8197 (tpt-90) cc_final: 0.6729 (tpt90) REVERT: M 166 GLN cc_start: 0.8912 (pt0) cc_final: 0.8480 (mm-40) REVERT: M 169 GLU cc_start: 0.8329 (mp0) cc_final: 0.7491 (tp30) REVERT: N 40 GLU cc_start: 0.6975 (pp20) cc_final: 0.5881 (mp0) REVERT: N 95 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8617 (mt-10) REVERT: N 101 MET cc_start: 0.8256 (tpt) cc_final: 0.7982 (tpt) REVERT: N 226 GLN cc_start: 0.7574 (mp10) cc_final: 0.7291 (mp10) REVERT: 2 212 MET cc_start: 0.7641 (mmp) cc_final: 0.7397 (mmp) REVERT: 2 294 LEU cc_start: 0.7804 (pt) cc_final: 0.7358 (pt) REVERT: 2 348 ILE cc_start: 0.8186 (pt) cc_final: 0.7735 (pt) REVERT: 2 527 ARG cc_start: 0.5368 (mmt180) cc_final: 0.4805 (mmm160) REVERT: 2 624 PRO cc_start: 0.7016 (Cg_endo) cc_final: 0.6454 (Cg_exo) REVERT: 2 630 GLU cc_start: 0.7895 (mp0) cc_final: 0.7544 (mp0) REVERT: 2 788 MET cc_start: 0.9053 (pmm) cc_final: 0.8781 (mmt) REVERT: 2 791 MET cc_start: 0.6090 (mmm) cc_final: 0.5788 (mmm) outliers start: 6 outliers final: 3 residues processed: 827 average time/residue: 0.5176 time to fit residues: 688.1844 Evaluate side-chains 668 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 665 time to evaluate : 4.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 451 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 266 optimal weight: 0.9980 chunk 341 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 394 optimal weight: 0.9980 chunk 261 optimal weight: 0.0870 chunk 466 optimal weight: 0.8980 chunk 291 optimal weight: 2.9990 chunk 284 optimal weight: 0.0670 chunk 215 optimal weight: 2.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS ** 4 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 699 HIS ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 115 HIS ** 6 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 231 GLN ** 6 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 HIS M 164 ASN ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 211 ASN ** 2 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 606 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.6831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 39744 Z= 0.177 Angle : 0.705 11.746 53737 Z= 0.357 Chirality : 0.045 0.196 6083 Planarity : 0.005 0.067 6914 Dihedral : 10.823 179.219 5609 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.66 % Favored : 88.29 % Rotamer: Outliers : 0.17 % Allowed : 1.95 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.63 (0.11), residues: 4775 helix: -1.89 (0.13), residues: 1415 sheet: -2.45 (0.23), residues: 444 loop : -2.80 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 47 HIS 0.013 0.001 HIS 7 459 PHE 0.034 0.002 PHE 7 77 TYR 0.034 0.001 TYR 7 33 ARG 0.008 0.001 ARG 7 589 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 797 time to evaluate : 4.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 125 GLU cc_start: 0.8704 (pm20) cc_final: 0.8355 (pm20) REVERT: 3 130 LYS cc_start: 0.4964 (mtpt) cc_final: 0.3897 (mptt) REVERT: 3 387 ARG cc_start: 0.6631 (ptm-80) cc_final: 0.6318 (ptm-80) REVERT: 3 405 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7235 (mp0) REVERT: 3 423 GLN cc_start: 0.7317 (tp40) cc_final: 0.6255 (pt0) REVERT: 3 627 MET cc_start: 0.8477 (ptp) cc_final: 0.6800 (ptp) REVERT: 3 628 SER cc_start: 0.7168 (m) cc_final: 0.6649 (p) REVERT: 4 226 TYR cc_start: 0.9112 (t80) cc_final: 0.8899 (t80) REVERT: 4 306 PHE cc_start: 0.6318 (t80) cc_final: 0.6015 (t80) REVERT: 4 345 ASN cc_start: 0.8383 (m110) cc_final: 0.8131 (t0) REVERT: 4 356 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7914 (ttmm) REVERT: 4 363 ASP cc_start: 0.8089 (t0) cc_final: 0.7831 (t0) REVERT: 4 371 HIS cc_start: 0.6099 (m-70) cc_final: 0.5624 (m-70) REVERT: 4 520 GLN cc_start: 0.8180 (tt0) cc_final: 0.7891 (mt0) REVERT: 4 758 LEU cc_start: 0.8465 (mp) cc_final: 0.8166 (tp) REVERT: 7 131 MET cc_start: 0.6436 (ptp) cc_final: 0.5888 (ptp) REVERT: 7 203 VAL cc_start: 0.7944 (m) cc_final: 0.7653 (t) REVERT: 7 242 ASP cc_start: 0.7999 (t0) cc_final: 0.7577 (t0) REVERT: 7 327 LEU cc_start: 0.8702 (tp) cc_final: 0.8462 (mt) REVERT: 7 369 MET cc_start: 0.6276 (tpt) cc_final: 0.5667 (mpp) REVERT: 7 559 MET cc_start: 0.7331 (mtp) cc_final: 0.6979 (mtp) REVERT: 7 619 LEU cc_start: 0.8156 (mt) cc_final: 0.7840 (tp) REVERT: 6 105 TYR cc_start: 0.5872 (m-80) cc_final: 0.5581 (t80) REVERT: 6 131 ILE cc_start: 0.8426 (pt) cc_final: 0.8147 (tp) REVERT: 6 223 ARG cc_start: 0.7879 (mtt180) cc_final: 0.7235 (tpp80) REVERT: 6 234 ASP cc_start: 0.5610 (m-30) cc_final: 0.5126 (m-30) REVERT: 6 288 MET cc_start: 0.7122 (tpp) cc_final: 0.6722 (tpt) REVERT: 6 317 MET cc_start: 0.5037 (tpt) cc_final: 0.4667 (tpp) REVERT: 6 442 MET cc_start: 0.5723 (ttt) cc_final: 0.4996 (ttt) REVERT: 6 503 ASP cc_start: 0.6355 (t70) cc_final: 0.5987 (t0) REVERT: 6 585 MET cc_start: 0.7999 (mmm) cc_final: 0.7279 (mmm) REVERT: 6 588 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8274 (mp0) REVERT: 5 32 LYS cc_start: 0.7478 (mmmm) cc_final: 0.7069 (mmtm) REVERT: 5 62 ARG cc_start: 0.7909 (mmt-90) cc_final: 0.7674 (mmt-90) REVERT: 5 171 SER cc_start: 0.7712 (m) cc_final: 0.7163 (p) REVERT: 5 246 ARG cc_start: 0.8236 (mtt90) cc_final: 0.7816 (tpt90) REVERT: 5 416 MET cc_start: 0.5973 (ppp) cc_final: 0.4964 (ptt) REVERT: 5 426 MET cc_start: 0.3761 (ppp) cc_final: 0.3546 (ppp) REVERT: 5 474 THR cc_start: 0.7843 (m) cc_final: 0.7383 (p) REVERT: 5 641 ARG cc_start: 0.8916 (mtt90) cc_final: 0.7878 (tmm-80) REVERT: A 8 ASN cc_start: 0.8741 (m-40) cc_final: 0.8530 (p0) REVERT: A 53 MET cc_start: 0.8524 (tpt) cc_final: 0.8214 (tpt) REVERT: A 229 ASN cc_start: 0.9046 (m-40) cc_final: 0.8690 (m110) REVERT: A 230 MET cc_start: 0.8149 (mtp) cc_final: 0.7844 (mtp) REVERT: A 243 GLN cc_start: 0.5943 (mm-40) cc_final: 0.5606 (tp40) REVERT: A 259 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8072 (mm-30) REVERT: A 276 ASN cc_start: 0.8007 (p0) cc_final: 0.7191 (t0) REVERT: A 347 LEU cc_start: 0.9145 (pp) cc_final: 0.8385 (tp) REVERT: A 368 ASP cc_start: 0.8829 (m-30) cc_final: 0.7965 (t0) REVERT: A 376 LEU cc_start: 0.5868 (tp) cc_final: 0.5454 (tp) REVERT: A 383 ARG cc_start: 0.7407 (mmt-90) cc_final: 0.7087 (mpt180) REVERT: A 469 PHE cc_start: 0.8621 (m-10) cc_final: 0.8386 (m-80) REVERT: A 513 MET cc_start: 0.3789 (mmp) cc_final: 0.2439 (mmt) REVERT: A 514 CYS cc_start: 0.6089 (m) cc_final: 0.5663 (t) REVERT: A 568 ASP cc_start: 0.8942 (m-30) cc_final: 0.8016 (t0) REVERT: H 35 ARG cc_start: 0.9069 (mmp80) cc_final: 0.8348 (ttp80) REVERT: H 75 GLN cc_start: 0.8998 (mm110) cc_final: 0.8538 (mm110) REVERT: H 90 ARG cc_start: 0.8735 (mtm-85) cc_final: 0.8499 (mtp85) REVERT: H 160 MET cc_start: 0.4170 (mtm) cc_final: 0.3152 (tpp) REVERT: L 70 ILE cc_start: 0.8880 (mt) cc_final: 0.8618 (mt) REVERT: L 109 ARG cc_start: 0.7805 (mmt180) cc_final: 0.6940 (ttt90) REVERT: L 125 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8255 (mt-10) REVERT: M 68 TYR cc_start: 0.7639 (m-10) cc_final: 0.7428 (m-10) REVERT: M 123 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7881 (mm-30) REVERT: M 126 ARG cc_start: 0.8318 (tpt-90) cc_final: 0.6961 (tpt90) REVERT: M 166 GLN cc_start: 0.8867 (pt0) cc_final: 0.8456 (mm-40) REVERT: M 169 GLU cc_start: 0.8379 (mp0) cc_final: 0.7641 (tp30) REVERT: N 40 GLU cc_start: 0.7039 (pp20) cc_final: 0.5907 (mp0) REVERT: N 86 ARG cc_start: 0.7575 (mtt-85) cc_final: 0.7233 (mtt-85) REVERT: N 95 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8663 (mt-10) REVERT: N 226 GLN cc_start: 0.7718 (mp10) cc_final: 0.7393 (mp10) REVERT: 2 294 LEU cc_start: 0.7775 (pt) cc_final: 0.7362 (pt) REVERT: 2 348 ILE cc_start: 0.8203 (pt) cc_final: 0.7912 (pt) REVERT: 2 358 TYR cc_start: 0.5227 (t80) cc_final: 0.4857 (t80) REVERT: 2 527 ARG cc_start: 0.5300 (mmt180) cc_final: 0.4710 (mmm160) REVERT: 2 624 PRO cc_start: 0.7208 (Cg_endo) cc_final: 0.6669 (Cg_exo) REVERT: 2 630 GLU cc_start: 0.7746 (mp0) cc_final: 0.7398 (mp0) REVERT: 2 660 LEU cc_start: 0.7056 (tt) cc_final: 0.6299 (mt) REVERT: 2 791 MET cc_start: 0.6123 (mmm) cc_final: 0.5823 (mmm) outliers start: 7 outliers final: 4 residues processed: 802 average time/residue: 0.5084 time to fit residues: 657.2881 Evaluate side-chains 648 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 644 time to evaluate : 4.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 288 optimal weight: 0.2980 chunk 186 optimal weight: 0.8980 chunk 278 optimal weight: 0.2980 chunk 140 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 317 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 366 optimal weight: 8.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS ** 4 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 115 HIS ** 6 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 456 HIS 5 563 HIS ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 HIS M 164 ASN N 110 GLN ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 211 ASN 2 450 GLN ** 2 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 548 ASN ** 2 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.7102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39744 Z= 0.171 Angle : 0.694 12.261 53737 Z= 0.350 Chirality : 0.044 0.201 6083 Planarity : 0.005 0.060 6914 Dihedral : 10.605 178.561 5609 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.39 % Favored : 88.59 % Rotamer: Outliers : 0.14 % Allowed : 1.28 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.55 (0.11), residues: 4775 helix: -1.83 (0.13), residues: 1420 sheet: -2.42 (0.22), residues: 470 loop : -2.73 (0.11), residues: 2885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 4 764 HIS 0.010 0.001 HIS 5 456 PHE 0.023 0.001 PHE N 115 TYR 0.023 0.001 TYR 2 358 ARG 0.009 0.000 ARG L 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 810 time to evaluate : 4.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3 125 GLU cc_start: 0.8693 (pm20) cc_final: 0.8386 (pm20) REVERT: 3 130 LYS cc_start: 0.5111 (mtpt) cc_final: 0.4011 (mptt) REVERT: 3 387 ARG cc_start: 0.6727 (ptm-80) cc_final: 0.6460 (ptm-80) REVERT: 3 405 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7258 (mp0) REVERT: 3 423 GLN cc_start: 0.7279 (tp40) cc_final: 0.6199 (pt0) REVERT: 3 611 THR cc_start: 0.7498 (p) cc_final: 0.7286 (p) REVERT: 3 628 SER cc_start: 0.7193 (m) cc_final: 0.6762 (p) REVERT: 4 306 PHE cc_start: 0.6118 (t80) cc_final: 0.5833 (t80) REVERT: 4 345 ASN cc_start: 0.8460 (m110) cc_final: 0.8105 (t0) REVERT: 4 356 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7825 (ttmm) REVERT: 4 363 ASP cc_start: 0.8085 (t0) cc_final: 0.7864 (t0) REVERT: 4 520 GLN cc_start: 0.8229 (tt0) cc_final: 0.7942 (mt0) REVERT: 4 707 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6801 (pm20) REVERT: 4 758 LEU cc_start: 0.8509 (mp) cc_final: 0.8227 (tp) REVERT: 7 174 LYS cc_start: 0.8858 (mmtm) cc_final: 0.8495 (mmtp) REVERT: 7 179 VAL cc_start: 0.6744 (p) cc_final: 0.6470 (m) REVERT: 7 203 VAL cc_start: 0.8207 (m) cc_final: 0.7965 (t) REVERT: 7 242 ASP cc_start: 0.7874 (t0) cc_final: 0.7428 (t0) REVERT: 7 327 LEU cc_start: 0.8652 (tp) cc_final: 0.8429 (mt) REVERT: 7 369 MET cc_start: 0.6384 (tpt) cc_final: 0.5626 (mpp) REVERT: 7 559 MET cc_start: 0.7213 (mtp) cc_final: 0.6892 (mtp) REVERT: 6 105 TYR cc_start: 0.5892 (m-80) cc_final: 0.5680 (t80) REVERT: 6 131 ILE cc_start: 0.8419 (pt) cc_final: 0.8115 (tp) REVERT: 6 223 ARG cc_start: 0.7848 (mtt180) cc_final: 0.7187 (tpp80) REVERT: 6 442 MET cc_start: 0.5861 (ttt) cc_final: 0.5114 (ttt) REVERT: 6 503 ASP cc_start: 0.6369 (t70) cc_final: 0.6016 (t0) REVERT: 6 588 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8283 (tm-30) REVERT: 6 592 HIS cc_start: 0.7874 (m90) cc_final: 0.7069 (t-90) REVERT: 5 32 LYS cc_start: 0.7458 (mmmm) cc_final: 0.7056 (mmtm) REVERT: 5 62 ARG cc_start: 0.7861 (mmt-90) cc_final: 0.7599 (mmt-90) REVERT: 5 86 GLN cc_start: 0.7083 (mp10) cc_final: 0.6820 (mp10) REVERT: 5 171 SER cc_start: 0.7781 (m) cc_final: 0.7232 (p) REVERT: 5 221 THR cc_start: 0.7993 (m) cc_final: 0.7752 (m) REVERT: 5 246 ARG cc_start: 0.8206 (mtt90) cc_final: 0.7817 (tpt90) REVERT: 5 416 MET cc_start: 0.6032 (ppp) cc_final: 0.5058 (ptt) REVERT: 5 426 MET cc_start: 0.3857 (ppp) cc_final: 0.3628 (ppp) REVERT: 5 456 HIS cc_start: 0.8257 (OUTLIER) cc_final: 0.8024 (t-90) REVERT: 5 474 THR cc_start: 0.7968 (m) cc_final: 0.7441 (p) REVERT: A 53 MET cc_start: 0.8485 (tpt) cc_final: 0.8184 (tpt) REVERT: A 55 VAL cc_start: 0.8463 (p) cc_final: 0.8255 (p) REVERT: A 229 ASN cc_start: 0.9047 (m-40) cc_final: 0.8701 (m110) REVERT: A 230 MET cc_start: 0.8134 (mtp) cc_final: 0.7813 (mtp) REVERT: A 243 GLN cc_start: 0.5946 (mm-40) cc_final: 0.5684 (tp40) REVERT: A 259 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8072 (mm-30) REVERT: A 276 ASN cc_start: 0.7831 (p0) cc_final: 0.7123 (t0) REVERT: A 330 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8261 (mt-10) REVERT: A 347 LEU cc_start: 0.9139 (pp) cc_final: 0.8398 (tp) REVERT: A 376 LEU cc_start: 0.6120 (tp) cc_final: 0.5681 (tp) REVERT: A 383 ARG cc_start: 0.7433 (mmt-90) cc_final: 0.7090 (mpt180) REVERT: A 469 PHE cc_start: 0.8614 (m-10) cc_final: 0.8386 (m-80) REVERT: A 513 MET cc_start: 0.3279 (mmp) cc_final: 0.1942 (mmt) REVERT: A 514 CYS cc_start: 0.6240 (m) cc_final: 0.5772 (t) REVERT: A 568 ASP cc_start: 0.8939 (m-30) cc_final: 0.7950 (t0) REVERT: H 35 ARG cc_start: 0.9073 (mmp80) cc_final: 0.8364 (ttp80) REVERT: H 75 GLN cc_start: 0.9021 (mm110) cc_final: 0.8617 (mm110) REVERT: H 145 ASN cc_start: -0.0327 (t0) cc_final: -0.0577 (m110) REVERT: H 160 MET cc_start: 0.4129 (mtm) cc_final: 0.3188 (tpp) REVERT: L 14 MET cc_start: 0.4390 (ttp) cc_final: 0.4021 (ttp) REVERT: L 70 ILE cc_start: 0.8789 (mt) cc_final: 0.8544 (mt) REVERT: L 109 ARG cc_start: 0.7768 (mmt180) cc_final: 0.6799 (ttt90) REVERT: L 112 GLU cc_start: 0.8277 (mp0) cc_final: 0.7002 (mp0) REVERT: L 125 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8191 (mp0) REVERT: L 146 ASP cc_start: 0.7600 (m-30) cc_final: 0.6851 (t70) REVERT: M 68 TYR cc_start: 0.7616 (m-10) cc_final: 0.7408 (m-10) REVERT: M 123 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7664 (mm-30) REVERT: M 126 ARG cc_start: 0.8214 (tpt-90) cc_final: 0.6813 (tpt90) REVERT: M 166 GLN cc_start: 0.8835 (pt0) cc_final: 0.8445 (mm-40) REVERT: M 169 GLU cc_start: 0.8376 (mp0) cc_final: 0.7603 (tp30) REVERT: N 40 GLU cc_start: 0.7015 (pp20) cc_final: 0.5884 (mp0) REVERT: N 95 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8762 (mt-10) REVERT: N 226 GLN cc_start: 0.7614 (mp10) cc_final: 0.7294 (mp10) REVERT: 2 294 LEU cc_start: 0.7746 (pt) cc_final: 0.7375 (pt) REVERT: 2 348 ILE cc_start: 0.8611 (pt) cc_final: 0.8235 (pt) REVERT: 2 358 TYR cc_start: 0.5177 (t80) cc_final: 0.4886 (t80) REVERT: 2 435 LYS cc_start: 0.8638 (tttm) cc_final: 0.8438 (tptm) REVERT: 2 466 MET cc_start: 0.3189 (ptm) cc_final: 0.2944 (ptt) REVERT: 2 527 ARG cc_start: 0.5100 (mmt180) cc_final: 0.4849 (mmm160) REVERT: 2 624 PRO cc_start: 0.7245 (Cg_endo) cc_final: 0.6758 (Cg_exo) REVERT: 2 630 GLU cc_start: 0.7730 (mp0) cc_final: 0.7374 (mp0) REVERT: 2 660 LEU cc_start: 0.7014 (tt) cc_final: 0.6255 (mt) outliers start: 6 outliers final: 3 residues processed: 814 average time/residue: 0.5112 time to fit residues: 668.3231 Evaluate side-chains 662 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 658 time to evaluate : 4.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 424 optimal weight: 0.9990 chunk 446 optimal weight: 2.9990 chunk 407 optimal weight: 3.9990 chunk 434 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 341 optimal weight: 0.0570 chunk 133 optimal weight: 2.9990 chunk 392 optimal weight: 0.5980 chunk 411 optimal weight: 0.9990 chunk 433 optimal weight: 1.9990 overall best weight: 0.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 260 ASN ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS 4 337 ASN ** 4 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 527 ASN 4 699 HIS ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 465 GLN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 115 HIS 6 181 ASN ** 6 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 HIS M 164 ASN ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 GLN ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 210 GLN 2 211 ASN ** 2 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 516 GLN 2 548 ASN ** 2 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.7371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 39744 Z= 0.195 Angle : 0.710 11.629 53737 Z= 0.360 Chirality : 0.045 0.192 6083 Planarity : 0.005 0.061 6914 Dihedral : 10.514 178.390 5609 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.98 % Favored : 88.00 % Rotamer: Outliers : 0.14 % Allowed : 0.88 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.47 (0.11), residues: 4775 helix: -1.74 (0.13), residues: 1426 sheet: -2.35 (0.23), residues: 449 loop : -2.71 (0.11), residues: 2900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 4 764 HIS 0.005 0.001 HIS 2 743 PHE 0.036 0.002 PHE A 535 TYR 0.028 0.002 TYR 2 358 ARG 0.009 0.001 ARG L 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 797 time to evaluate : 4.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3 125 GLU cc_start: 0.8594 (pm20) cc_final: 0.8120 (pm20) REVERT: 3 130 LYS cc_start: 0.5194 (mtpt) cc_final: 0.4077 (mptt) REVERT: 3 179 ASN cc_start: 0.7448 (m110) cc_final: 0.7147 (t0) REVERT: 3 227 LYS cc_start: 0.5595 (ptpp) cc_final: 0.5260 (pttm) REVERT: 3 239 ARG cc_start: 0.4872 (mtt90) cc_final: 0.4641 (mtp-110) REVERT: 3 387 ARG cc_start: 0.6694 (ptm-80) cc_final: 0.6465 (ptm-80) REVERT: 3 405 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7207 (mp0) REVERT: 3 628 SER cc_start: 0.7235 (m) cc_final: 0.6817 (p) REVERT: 4 226 TYR cc_start: 0.9059 (t80) cc_final: 0.8777 (t80) REVERT: 4 306 PHE cc_start: 0.6203 (t80) cc_final: 0.5933 (t80) REVERT: 4 345 ASN cc_start: 0.8511 (m110) cc_final: 0.8185 (t0) REVERT: 4 356 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7839 (ttmm) REVERT: 4 520 GLN cc_start: 0.8294 (tt0) cc_final: 0.7944 (mt0) REVERT: 4 577 GLU cc_start: 0.7408 (tp30) cc_final: 0.6090 (tp30) REVERT: 4 580 LYS cc_start: 0.6989 (mppt) cc_final: 0.6744 (mmtm) REVERT: 4 591 GLU cc_start: 0.6770 (tp30) cc_final: 0.6521 (tp30) REVERT: 4 707 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6824 (pm20) REVERT: 4 758 LEU cc_start: 0.8535 (mp) cc_final: 0.8256 (tp) REVERT: 7 20 PHE cc_start: 0.6891 (t80) cc_final: 0.3719 (t80) REVERT: 7 179 VAL cc_start: 0.6643 (p) cc_final: 0.6295 (m) REVERT: 7 203 VAL cc_start: 0.8384 (m) cc_final: 0.8067 (t) REVERT: 7 242 ASP cc_start: 0.7968 (t0) cc_final: 0.7475 (t0) REVERT: 7 369 MET cc_start: 0.6664 (tpt) cc_final: 0.5911 (mpp) REVERT: 7 559 MET cc_start: 0.7291 (mtp) cc_final: 0.6998 (mtp) REVERT: 6 105 TYR cc_start: 0.6015 (m-80) cc_final: 0.5617 (t80) REVERT: 6 131 ILE cc_start: 0.8423 (pt) cc_final: 0.8090 (tp) REVERT: 6 223 ARG cc_start: 0.7744 (mtt180) cc_final: 0.7050 (tpp80) REVERT: 6 288 MET cc_start: 0.7201 (tpt) cc_final: 0.6162 (tpt) REVERT: 6 354 ASP cc_start: 0.5590 (m-30) cc_final: 0.4922 (t70) REVERT: 6 442 MET cc_start: 0.5743 (ttt) cc_final: 0.4872 (ttt) REVERT: 6 503 ASP cc_start: 0.6394 (t70) cc_final: 0.6026 (t0) REVERT: 6 588 GLU cc_start: 0.8568 (tm-30) cc_final: 0.7963 (tm-30) REVERT: 5 32 LYS cc_start: 0.7497 (mmmm) cc_final: 0.7104 (mmtm) REVERT: 5 47 PHE cc_start: 0.3251 (m-80) cc_final: 0.2672 (m-80) REVERT: 5 86 GLN cc_start: 0.7272 (mp10) cc_final: 0.7010 (mp10) REVERT: 5 115 HIS cc_start: 0.7776 (p90) cc_final: 0.7433 (p90) REVERT: 5 171 SER cc_start: 0.7890 (m) cc_final: 0.7377 (p) REVERT: 5 210 MET cc_start: 0.7793 (tpt) cc_final: 0.7402 (tpp) REVERT: 5 246 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7928 (tpt90) REVERT: 5 416 MET cc_start: 0.5811 (ppp) cc_final: 0.4903 (ptt) REVERT: 5 426 MET cc_start: 0.3403 (ppp) cc_final: 0.3164 (ppp) REVERT: 5 474 THR cc_start: 0.8110 (m) cc_final: 0.7650 (p) REVERT: 5 641 ARG cc_start: 0.8801 (mpp-170) cc_final: 0.7328 (tmm-80) REVERT: A 53 MET cc_start: 0.8596 (tpt) cc_final: 0.8286 (tpt) REVERT: A 229 ASN cc_start: 0.9095 (m-40) cc_final: 0.8792 (m110) REVERT: A 230 MET cc_start: 0.8219 (mtp) cc_final: 0.7942 (mtp) REVERT: A 243 GLN cc_start: 0.5917 (mm-40) cc_final: 0.5671 (tp40) REVERT: A 259 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8101 (mm-30) REVERT: A 276 ASN cc_start: 0.7620 (p0) cc_final: 0.7041 (t0) REVERT: A 330 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8397 (mt-10) REVERT: A 347 LEU cc_start: 0.9188 (pp) cc_final: 0.8402 (tp) REVERT: A 383 ARG cc_start: 0.7356 (mmt-90) cc_final: 0.6976 (mpt180) REVERT: A 513 MET cc_start: 0.3665 (mmp) cc_final: 0.3148 (mmt) REVERT: A 568 ASP cc_start: 0.8951 (m-30) cc_final: 0.7990 (t0) REVERT: H 35 ARG cc_start: 0.9057 (mmp80) cc_final: 0.8542 (ttp80) REVERT: H 42 LYS cc_start: 0.8638 (mttt) cc_final: 0.8106 (mtmm) REVERT: H 145 ASN cc_start: -0.0143 (t0) cc_final: -0.0580 (m110) REVERT: H 160 MET cc_start: 0.4074 (mtm) cc_final: 0.3155 (tpp) REVERT: L 70 ILE cc_start: 0.8988 (mt) cc_final: 0.8682 (mt) REVERT: L 100 MET cc_start: 0.9178 (mmm) cc_final: 0.8925 (mmm) REVERT: L 109 ARG cc_start: 0.7765 (mmt180) cc_final: 0.7018 (ttm-80) REVERT: L 112 GLU cc_start: 0.8207 (mp0) cc_final: 0.6819 (mp0) REVERT: L 125 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8281 (mt-10) REVERT: L 146 ASP cc_start: 0.7724 (m-30) cc_final: 0.6901 (t70) REVERT: L 183 MET cc_start: 0.5811 (tpt) cc_final: 0.5531 (tpt) REVERT: M 68 TYR cc_start: 0.7669 (m-10) cc_final: 0.7456 (m-10) REVERT: M 123 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7755 (mm-30) REVERT: M 126 ARG cc_start: 0.8362 (tpt-90) cc_final: 0.6920 (tpt90) REVERT: M 166 GLN cc_start: 0.8867 (pt0) cc_final: 0.8437 (mm-40) REVERT: M 169 GLU cc_start: 0.8326 (mp0) cc_final: 0.7736 (tp30) REVERT: N 40 GLU cc_start: 0.7046 (pp20) cc_final: 0.5993 (mp0) REVERT: N 95 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8559 (mt-10) REVERT: N 226 GLN cc_start: 0.7383 (mp10) cc_final: 0.6942 (mp10) REVERT: 2 348 ILE cc_start: 0.8674 (pt) cc_final: 0.8219 (pt) REVERT: 2 527 ARG cc_start: 0.5016 (mmt180) cc_final: 0.4771 (mmm160) REVERT: 2 624 PRO cc_start: 0.7134 (Cg_endo) cc_final: 0.6604 (Cg_exo) REVERT: 2 630 GLU cc_start: 0.7791 (mp0) cc_final: 0.7404 (mp0) REVERT: 2 660 LEU cc_start: 0.7012 (tt) cc_final: 0.6201 (mt) REVERT: 2 669 MET cc_start: 0.4480 (ptp) cc_final: 0.4239 (ptt) REVERT: 2 791 MET cc_start: 0.5718 (mmm) cc_final: 0.5301 (mpp) outliers start: 6 outliers final: 3 residues processed: 801 average time/residue: 0.5209 time to fit residues: 670.2030 Evaluate side-chains 652 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 649 time to evaluate : 4.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 285 optimal weight: 0.0370 chunk 459 optimal weight: 0.0970 chunk 280 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 319 optimal weight: 0.8980 chunk 482 optimal weight: 0.7980 chunk 443 optimal weight: 4.9990 chunk 383 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 296 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS ** 4 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 699 HIS ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 206 GLN ** 6 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 261 GLN 5 456 HIS 5 563 HIS ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 HIS M 164 ASN N 110 GLN 2 211 ASN ** 2 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.7627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 39744 Z= 0.176 Angle : 0.693 11.815 53737 Z= 0.349 Chirality : 0.044 0.194 6083 Planarity : 0.005 0.079 6914 Dihedral : 10.358 177.911 5609 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.37 % Favored : 88.61 % Rotamer: Outliers : 0.14 % Allowed : 0.38 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.42 (0.11), residues: 4775 helix: -1.71 (0.13), residues: 1438 sheet: -2.28 (0.23), residues: 458 loop : -2.68 (0.11), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 4 764 HIS 0.009 0.001 HIS 5 456 PHE 0.031 0.002 PHE 5 643 TYR 0.036 0.001 TYR 3 16 ARG 0.008 0.000 ARG 6 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 785 time to evaluate : 4.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 3 18 ASP cc_start: 0.8763 (m-30) cc_final: 0.8501 (t0) REVERT: 3 36 MET cc_start: 0.7390 (tpt) cc_final: 0.7153 (mmm) REVERT: 3 125 GLU cc_start: 0.8686 (pm20) cc_final: 0.8316 (pm20) REVERT: 3 130 LYS cc_start: 0.5142 (mtpt) cc_final: 0.4052 (mptt) REVERT: 3 179 ASN cc_start: 0.7510 (m110) cc_final: 0.7164 (m-40) REVERT: 3 239 ARG cc_start: 0.5029 (mtt90) cc_final: 0.4825 (mtp-110) REVERT: 3 405 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7229 (mp0) REVERT: 3 425 ARG cc_start: 0.8455 (ptm160) cc_final: 0.7750 (mtm110) REVERT: 3 624 ARG cc_start: 0.5513 (tpt170) cc_final: 0.5005 (tpt90) REVERT: 3 628 SER cc_start: 0.7181 (m) cc_final: 0.6788 (p) REVERT: 4 249 PHE cc_start: 0.8362 (m-10) cc_final: 0.8040 (t80) REVERT: 4 282 MET cc_start: 0.8597 (tpp) cc_final: 0.8268 (tpp) REVERT: 4 306 PHE cc_start: 0.6278 (t80) cc_final: 0.5879 (t80) REVERT: 4 356 LYS cc_start: 0.8013 (ttmm) cc_final: 0.7811 (ttmm) REVERT: 4 371 HIS cc_start: 0.6567 (m-70) cc_final: 0.6353 (m170) REVERT: 4 520 GLN cc_start: 0.8270 (tt0) cc_final: 0.7950 (mt0) REVERT: 4 577 GLU cc_start: 0.7020 (tp30) cc_final: 0.5837 (tp30) REVERT: 4 591 GLU cc_start: 0.6696 (tp30) cc_final: 0.6099 (tp30) REVERT: 4 698 GLU cc_start: 0.7108 (tt0) cc_final: 0.6385 (tt0) REVERT: 4 707 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6830 (pm20) REVERT: 4 713 ILE cc_start: 0.8098 (mt) cc_final: 0.7846 (mm) REVERT: 4 758 LEU cc_start: 0.8498 (mp) cc_final: 0.8236 (tp) REVERT: 7 174 LYS cc_start: 0.8827 (mmtm) cc_final: 0.8468 (mmtp) REVERT: 7 203 VAL cc_start: 0.8334 (m) cc_final: 0.8012 (t) REVERT: 7 242 ASP cc_start: 0.7946 (t0) cc_final: 0.7460 (t0) REVERT: 7 302 ARG cc_start: 0.8037 (ttt-90) cc_final: 0.7814 (ttt-90) REVERT: 7 369 MET cc_start: 0.6763 (tpt) cc_final: 0.5997 (mpp) REVERT: 7 559 MET cc_start: 0.7298 (mtp) cc_final: 0.7038 (mtp) REVERT: 7 598 MET cc_start: 0.3532 (mmm) cc_final: 0.3150 (mtp) REVERT: 6 105 TYR cc_start: 0.5816 (m-80) cc_final: 0.5506 (t80) REVERT: 6 131 ILE cc_start: 0.8512 (pt) cc_final: 0.8166 (tp) REVERT: 6 223 ARG cc_start: 0.7627 (mtt180) cc_final: 0.6984 (tpp80) REVERT: 6 288 MET cc_start: 0.7374 (tpt) cc_final: 0.6583 (tpt) REVERT: 6 354 ASP cc_start: 0.5447 (m-30) cc_final: 0.4796 (t70) REVERT: 6 442 MET cc_start: 0.5724 (ttt) cc_final: 0.5000 (ttt) REVERT: 6 460 ARG cc_start: 0.8510 (mpt90) cc_final: 0.8213 (mpt90) REVERT: 6 503 ASP cc_start: 0.6394 (t70) cc_final: 0.6014 (t0) REVERT: 6 585 MET cc_start: 0.8127 (mmp) cc_final: 0.7583 (mmm) REVERT: 6 588 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8321 (mp0) REVERT: 5 32 LYS cc_start: 0.7486 (mmmm) cc_final: 0.7067 (mmtm) REVERT: 5 62 ARG cc_start: 0.7951 (mmt-90) cc_final: 0.7150 (mtt90) REVERT: 5 86 GLN cc_start: 0.7250 (mp10) cc_final: 0.6970 (mp10) REVERT: 5 171 SER cc_start: 0.7891 (m) cc_final: 0.7355 (p) REVERT: 5 210 MET cc_start: 0.7656 (tpt) cc_final: 0.7340 (tpp) REVERT: 5 416 MET cc_start: 0.5807 (ppp) cc_final: 0.4801 (ptm) REVERT: 5 426 MET cc_start: 0.3367 (ppp) cc_final: 0.3134 (ppp) REVERT: 5 456 HIS cc_start: 0.8381 (OUTLIER) cc_final: 0.8156 (t-90) REVERT: 5 474 THR cc_start: 0.8221 (m) cc_final: 0.7753 (p) REVERT: 5 641 ARG cc_start: 0.8787 (mpp-170) cc_final: 0.7503 (ptm160) REVERT: A 53 MET cc_start: 0.8593 (tpt) cc_final: 0.8297 (tpt) REVERT: A 229 ASN cc_start: 0.9089 (m-40) cc_final: 0.8787 (m110) REVERT: A 230 MET cc_start: 0.8189 (mtp) cc_final: 0.7875 (mtp) REVERT: A 259 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8118 (mm-30) REVERT: A 276 ASN cc_start: 0.7625 (p0) cc_final: 0.7090 (t0) REVERT: A 347 LEU cc_start: 0.9153 (pp) cc_final: 0.8390 (tp) REVERT: A 376 LEU cc_start: 0.6098 (tp) cc_final: 0.5690 (tp) REVERT: A 383 ARG cc_start: 0.7380 (mmt-90) cc_final: 0.7030 (mpt180) REVERT: A 494 ARG cc_start: 0.2878 (tpt170) cc_final: 0.1568 (tpm170) REVERT: A 513 MET cc_start: 0.3513 (mmp) cc_final: 0.3093 (mmt) REVERT: A 568 ASP cc_start: 0.8942 (m-30) cc_final: 0.7982 (t0) REVERT: H 35 ARG cc_start: 0.9105 (mmp80) cc_final: 0.8595 (ttp80) REVERT: H 42 LYS cc_start: 0.8707 (mttt) cc_final: 0.8261 (mtmm) REVERT: H 75 GLN cc_start: 0.9031 (mm110) cc_final: 0.8601 (mm110) REVERT: H 145 ASN cc_start: -0.0367 (t0) cc_final: -0.0721 (m110) REVERT: H 160 MET cc_start: 0.4009 (mtm) cc_final: 0.3141 (tpp) REVERT: L 14 MET cc_start: 0.3962 (ttp) cc_final: 0.3401 (mtp) REVERT: L 43 PHE cc_start: 0.7502 (p90) cc_final: 0.6957 (p90) REVERT: L 70 ILE cc_start: 0.8948 (mt) cc_final: 0.8628 (mt) REVERT: L 100 MET cc_start: 0.9150 (mmm) cc_final: 0.8890 (mmm) REVERT: L 109 ARG cc_start: 0.7799 (mmt180) cc_final: 0.6983 (ttm-80) REVERT: L 112 GLU cc_start: 0.8207 (mp0) cc_final: 0.6848 (mp0) REVERT: L 125 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8221 (mt-10) REVERT: L 146 ASP cc_start: 0.7715 (m-30) cc_final: 0.6896 (t70) REVERT: M 34 MET cc_start: 0.7169 (tmm) cc_final: 0.6841 (tmm) REVERT: M 68 TYR cc_start: 0.7657 (m-10) cc_final: 0.7446 (m-10) REVERT: M 123 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7530 (mm-30) REVERT: M 126 ARG cc_start: 0.8170 (tpt-90) cc_final: 0.6770 (tpt90) REVERT: M 166 GLN cc_start: 0.8841 (pt0) cc_final: 0.8352 (mp10) REVERT: M 169 GLU cc_start: 0.8333 (mp0) cc_final: 0.7620 (tp30) REVERT: N 40 GLU cc_start: 0.6984 (pp20) cc_final: 0.5883 (mp0) REVERT: N 95 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8722 (mt-10) REVERT: N 226 GLN cc_start: 0.7693 (mp10) cc_final: 0.7324 (mp10) REVERT: 2 348 ILE cc_start: 0.8652 (pt) cc_final: 0.8308 (pt) REVERT: 2 466 MET cc_start: 0.2744 (ptt) cc_final: 0.2198 (ptt) REVERT: 2 624 PRO cc_start: 0.7025 (Cg_endo) cc_final: 0.6477 (Cg_exo) REVERT: 2 630 GLU cc_start: 0.7800 (mp0) cc_final: 0.7416 (mp0) REVERT: 2 660 LEU cc_start: 0.6926 (tt) cc_final: 0.6109 (mt) REVERT: 2 791 MET cc_start: 0.5741 (mmm) cc_final: 0.5384 (mpp) outliers start: 6 outliers final: 3 residues processed: 789 average time/residue: 0.5002 time to fit residues: 639.5574 Evaluate side-chains 655 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 651 time to evaluate : 3.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 304 optimal weight: 5.9990 chunk 409 optimal weight: 0.0060 chunk 117 optimal weight: 3.9990 chunk 354 optimal weight: 0.0060 chunk 56 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 384 optimal weight: 2.9990 chunk 160 optimal weight: 0.4980 chunk 394 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 0.0980 overall best weight: 0.3012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS ** 4 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 353 GLN 4 500 GLN ** 4 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 465 GLN 7 557 ASN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 181 ASN ** 6 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 261 GLN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 HIS H 199 HIS M 164 ASN ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 GLN 2 211 ASN ** 2 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 666 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.220123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.203305 restraints weight = 109351.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.204122 restraints weight = 89666.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.204589 restraints weight = 75848.694| |-----------------------------------------------------------------------------| r_work (final): 0.4608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.7900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39744 Z= 0.166 Angle : 0.684 11.453 53737 Z= 0.343 Chirality : 0.044 0.190 6083 Planarity : 0.005 0.073 6914 Dihedral : 10.150 178.206 5609 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.43 % Favored : 88.54 % Rotamer: Outliers : 0.12 % Allowed : 0.52 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.31 (0.11), residues: 4775 helix: -1.60 (0.13), residues: 1444 sheet: -2.14 (0.23), residues: 445 loop : -2.64 (0.11), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 4 764 HIS 0.006 0.001 HIS 6 79 PHE 0.027 0.001 PHE 5 643 TYR 0.023 0.001 TYR N 99 ARG 0.008 0.000 ARG 6 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11401.75 seconds wall clock time: 204 minutes 23.79 seconds (12263.79 seconds total)