Starting phenix.real_space_refine on Fri Feb 23 01:07:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zjl_11235/02_2024/6zjl_11235_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zjl_11235/02_2024/6zjl_11235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zjl_11235/02_2024/6zjl_11235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zjl_11235/02_2024/6zjl_11235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zjl_11235/02_2024/6zjl_11235_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zjl_11235/02_2024/6zjl_11235_updated.pdb" } resolution = 4.3 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= 0.039 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: 6 Type Number sf(0) Gaussians Fe 32 7.16 5 P 1 5.49 5 S 180 5.16 5 C 23625 2.51 5 N 5998 2.21 5 O 6221 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ASP 10": "OD1" <-> "OD2" Residue "1 TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 24": "OE1" <-> "OE2" Residue "1 ASP 30": "OD1" <-> "OD2" Residue "1 GLU 55": "OE1" <-> "OE2" Residue "1 GLU 56": "OE1" <-> "OE2" Residue "1 PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 83": "OD1" <-> "OD2" Residue "1 GLU 95": "OE1" <-> "OE2" Residue "1 ASP 103": "OD1" <-> "OD2" Residue "1 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 137": "OE1" <-> "OE2" Residue "1 TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 146": "OE1" <-> "OE2" Residue "1 ASP 166": "OD1" <-> "OD2" Residue "1 ASP 170": "OD1" <-> "OD2" Residue "1 GLU 185": "OE1" <-> "OE2" Residue "1 GLU 232": "OE1" <-> "OE2" Residue "1 TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 278": "OE1" <-> "OE2" Residue "1 GLU 305": "OE1" <-> "OE2" Residue "1 TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 339": "OD1" <-> "OD2" Residue "1 PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 351": "OE1" <-> "OE2" Residue "1 GLU 380": "OE1" <-> "OE2" Residue "1 ASP 383": "OD1" <-> "OD2" Residue "1 GLU 385": "OE1" <-> "OE2" Residue "1 PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 419": "OD1" <-> "OD2" Residue "2 PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 13": "OE1" <-> "OE2" Residue "2 GLU 21": "OE1" <-> "OE2" Residue "2 GLU 37": "OE1" <-> "OE2" Residue "2 GLU 47": "OE1" <-> "OE2" Residue "2 GLU 59": "OE1" <-> "OE2" Residue "2 GLU 94": "OE1" <-> "OE2" Residue "2 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 102": "OE1" <-> "OE2" Residue "2 ASP 114": "OD1" <-> "OD2" Residue "2 GLU 123": "OE1" <-> "OE2" Residue "2 TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 143": "OE1" <-> "OE2" Residue "2 GLU 151": "OE1" <-> "OE2" Residue "2 GLU 164": "OE1" <-> "OE2" Residue "2 GLU 165": "OE1" <-> "OE2" Residue "2 GLU 167": "OE1" <-> "OE2" Residue "2 GLU 178": "OE1" <-> "OE2" Residue "3 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 94": "OD1" <-> "OD2" Residue "3 ASP 98": "OD1" <-> "OD2" Residue "3 ASP 132": "OD1" <-> "OD2" Residue "3 GLU 136": "OE1" <-> "OE2" Residue "3 GLU 141": "OE1" <-> "OE2" Residue "3 TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 158": "OE1" <-> "OE2" Residue "3 PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 165": "OD1" <-> "OD2" Residue "3 ASP 177": "OD1" <-> "OD2" Residue "3 ASP 197": "OD1" <-> "OD2" Residue "3 PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 215": "OD1" <-> "OD2" Residue "3 GLU 248": "OE1" <-> "OE2" Residue "3 GLU 250": "OE1" <-> "OE2" Residue "3 ASP 268": "OD1" <-> "OD2" Residue "3 GLU 287": "OE1" <-> "OE2" Residue "3 ASP 292": "OD1" <-> "OD2" Residue "3 GLU 324": "OE1" <-> "OE2" Residue "3 GLU 331": "OE1" <-> "OE2" Residue "3 GLU 339": "OE1" <-> "OE2" Residue "3 GLU 340": "OE1" <-> "OE2" Residue "3 GLU 352": "OE1" <-> "OE2" Residue "3 GLU 359": "OE1" <-> "OE2" Residue "3 ASP 370": "OD1" <-> "OD2" Residue "3 PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 389": "OD1" <-> "OD2" Residue "3 ASP 401": "OD1" <-> "OD2" Residue "3 GLU 404": "OE1" <-> "OE2" Residue "3 TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 434": "OD1" <-> "OD2" Residue "3 GLU 439": "OE1" <-> "OE2" Residue "3 ASP 483": "OD1" <-> "OD2" Residue "3 GLU 485": "OE1" <-> "OE2" Residue "3 GLU 526": "OE1" <-> "OE2" Residue "3 GLU 560": "OE1" <-> "OE2" Residue "3 GLU 595": "OE1" <-> "OE2" Residue "3 GLU 630": "OE1" <-> "OE2" Residue "3 GLU 671": "OE1" <-> "OE2" Residue "3 PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 682": "OE1" <-> "OE2" Residue "3 GLU 687": "OE1" <-> "OE2" Residue "3 GLU 726": "OE1" <-> "OE2" Residue "3 GLU 730": "OE1" <-> "OE2" Residue "3 GLU 737": "OE1" <-> "OE2" Residue "3 PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 744": "OE1" <-> "OE2" Residue "4 GLU 50": "OE1" <-> "OE2" Residue "4 GLU 54": "OE1" <-> "OE2" Residue "4 ASP 139": "OD1" <-> "OD2" Residue "4 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 158": "OD1" <-> "OD2" Residue "4 PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 180": "OE1" <-> "OE2" Residue "4 GLU 189": "OE1" <-> "OE2" Residue "4 GLU 203": "OE1" <-> "OE2" Residue "4 GLU 205": "OE1" <-> "OE2" Residue "4 PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 210": "OE1" <-> "OE2" Residue "4 PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 247": "OD1" <-> "OD2" Residue "4 TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 258": "OE1" <-> "OE2" Residue "4 TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 263": "OD1" <-> "OD2" Residue "4 GLU 268": "OE1" <-> "OE2" Residue "4 ASP 274": "OD1" <-> "OD2" Residue "4 GLU 282": "OE1" <-> "OE2" Residue "4 GLU 295": "OE1" <-> "OE2" Residue "4 ASP 304": "OD1" <-> "OD2" Residue "4 TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 333": "OE1" <-> "OE2" Residue "4 PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 360": "OD1" <-> "OD2" Residue "4 PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 392": "OD1" <-> "OD2" Residue "5 ASP 19": "OD1" <-> "OD2" Residue "5 GLU 36": "OE1" <-> "OE2" Residue "5 GLU 37": "OE1" <-> "OE2" Residue "5 PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 51": "OD1" <-> "OD2" Residue "5 ASP 56": "OD1" <-> "OD2" Residue "5 TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 62": "OD1" <-> "OD2" Residue "5 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 84": "OD1" <-> "OD2" Residue "5 TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 96": "OE1" <-> "OE2" Residue "5 GLU 97": "OE1" <-> "OE2" Residue "5 ASP 98": "OD1" <-> "OD2" Residue "5 ASP 106": "OD1" <-> "OD2" Residue "5 GLU 117": "OE1" <-> "OE2" Residue "5 PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 139": "OE1" <-> "OE2" Residue "5 ASP 140": "OD1" <-> "OD2" Residue "5 GLU 142": "OE1" <-> "OE2" Residue "5 TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 154": "OE1" <-> "OE2" Residue "5 PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 161": "OE1" <-> "OE2" Residue "5 GLU 169": "OE1" <-> "OE2" Residue "5 PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 25": "OE1" <-> "OE2" Residue "6 ASP 59": "OD1" <-> "OD2" Residue "6 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 76": "OD1" <-> "OD2" Residue "6 TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 128": "OD1" <-> "OD2" Residue "6 ASP 134": "OD1" <-> "OD2" Residue "6 GLU 145": "OE1" <-> "OE2" Residue "9 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 74": "OE1" <-> "OE2" Residue "9 GLU 78": "OE1" <-> "OE2" Residue "9 GLU 85": "OE1" <-> "OE2" Residue "9 TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 92": "OE1" <-> "OE2" Residue "9 PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 105": "OE1" <-> "OE2" Residue "9 GLU 106": "OE1" <-> "OE2" Residue "9 ASP 118": "OD1" <-> "OD2" Residue "9 PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 125": "OE1" <-> "OE2" Residue "9 ASP 128": "OD1" <-> "OD2" Residue "9 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 135": "OD1" <-> "OD2" Residue "9 ASP 139": "OD1" <-> "OD2" Residue "9 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 171": "OE1" <-> "OE2" Residue "7 GLU 11": "OE1" <-> "OE2" Residue "7 GLU 22": "OE1" <-> "OE2" Residue "7 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 36": "OD1" <-> "OD2" Residue "7 ASP 61": "OD1" <-> "OD2" Residue "7 GLU 65": "OE1" <-> "OE2" Residue "7 ASP 71": "OD1" <-> "OD2" Residue "7 GLU 98": "OE1" <-> "OE2" Residue "7 PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 120": "OD1" <-> "OD2" Residue "7 GLU 124": "OE1" <-> "OE2" Residue "7 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 49": "OD1" <-> "OD2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 5": "OE1" <-> "OE2" Residue "J PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J ASP 84": "OD1" <-> "OD2" Residue "J PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "K TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 88": "OD1" <-> "OD2" Residue "L PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 98": "OD1" <-> "OD2" Residue "L TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "L TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L GLU 190": "OE1" <-> "OE2" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 265": "OD1" <-> "OD2" Residue "L TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 290": "OD1" <-> "OD2" Residue "L PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 346": "OE1" <-> "OE2" Residue "L ASP 348": "OD1" <-> "OD2" Residue "L TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 429": "OE1" <-> "OE2" Residue "L GLU 470": "OE1" <-> "OE2" Residue "L GLU 490": "OE1" <-> "OE2" Residue "L PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 530": "OE1" <-> "OE2" Residue "L PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 535": "OD1" <-> "OD2" Residue "L GLU 551": "OE1" <-> "OE2" Residue "L TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 557": "OD1" <-> "OD2" Residue "L TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "M PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "M GLU 139": "OE1" <-> "OE2" Residue "M GLU 178": "OE1" <-> "OE2" Residue "M ASP 179": "OD1" <-> "OD2" Residue "M GLU 188": "OE1" <-> "OE2" Residue "M GLU 220": "OE1" <-> "OE2" Residue "M GLU 251": "OE1" <-> "OE2" Residue "M PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 280": "OD1" <-> "OD2" Residue "M TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 334": "OE1" <-> "OE2" Residue "M PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 417": "OE1" <-> "OE2" Residue "M ASP 424": "OD1" <-> "OD2" Residue "M GLU 429": "OE1" <-> "OE2" Residue "M PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 459": "OE1" <-> "OE2" Residue "N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 83": "OE1" <-> "OE2" Residue "N GLU 112": "OE1" <-> "OE2" Residue "N ASP 198": "OD1" <-> "OD2" Residue "N PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 225": "NH1" <-> "NH2" Residue "N PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 310": "OE1" <-> "OE2" Residue "N TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 319": "OD1" <-> "OD2" Residue "N GLU 351": "OE1" <-> "OE2" Residue "N TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 387": "OE1" <-> "OE2" Residue "H ASP 8": "OD1" <-> "OD2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 62": "OD1" <-> "OD2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H ASP 78": "OD1" <-> "OD2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 119": "OD1" <-> "OD2" Residue "H PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 184": "OD1" <-> "OD2" Residue "H GLU 191": "OE1" <-> "OE2" Residue "H TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 235": "OE1" <-> "OE2" Residue "H TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 273": "OE1" <-> "OE2" Residue "H PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.27s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36057 Number of models: 1 Model: "" Number of chains: 20 Chain: "1" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3417 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 405} Chain: "2" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1406 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "3" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5876 Classifications: {'peptide': 754} Link IDs: {'PTRANS': 53, 'TRANS': 700} Chain breaks: 2 Chain: "4" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3067 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 353} Chain: "5" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1607 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 16, 'TRANS': 179} Chain: "6" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1289 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 153} Chain: "9" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 163} Chain: "7" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1031 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 118} Chain: "A" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "J" Number of atoms: 1183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1183 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "K" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 703 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'TRANS': 94} Chain: "L" Number of atoms: 4604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4604 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 575} Chain: "M" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3489 Classifications: {'peptide': 467} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain: "N" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3154 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 401} Chain: "H" Number of atoms: 2838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2838 Classifications: {'peptide': 353} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 333} Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Unusual residues: {'FES': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2772 SG CYS 1 356 113.472 70.680 223.270 1.00 50.00 S ATOM 2792 SG CYS 1 359 117.693 72.814 225.970 1.00 50.00 S ATOM 3102 SG CYS 1 400 112.357 70.375 228.915 1.00 50.00 S ATOM 2753 SG CYS 1 353 116.038 66.609 226.824 1.00 50.00 S ATOM 4091 SG CYS 2 83 128.181 73.951 243.535 1.00 50.00 S ATOM 4123 SG CYS 2 88 129.412 76.425 245.982 1.00 50.00 S ATOM 4394 SG CYS 2 124 123.487 74.850 243.815 1.00 50.00 S ATOM 4418 SG CYS 2 128 123.505 77.246 246.365 1.00 50.00 S ATOM 5640 SG CYS 3 128 121.009 66.516 203.662 1.00 50.00 S ATOM 5584 SG CYS 3 119 125.918 69.768 201.811 1.00 50.00 S ATOM 5604 SG CYS 3 122 126.520 63.777 203.146 1.00 50.00 S ATOM 6083 SG CYS 3 184 115.923 61.659 213.032 1.00 50.00 S ATOM 6059 SG CYS 3 181 122.185 62.242 214.338 1.00 50.00 S ATOM 6109 SG CYS 3 187 118.661 56.979 214.324 1.00 50.00 S ATOM 6445 SG CYS 3 230 120.037 60.271 209.043 1.00 50.00 S ATOM 6652 SG CYS 3 256 112.923 41.114 197.082 1.00 50.00 S ATOM 6918 SG CYS 3 291 114.235 40.927 203.195 1.00 50.00 S ATOM 6695 SG CYS 3 263 108.931 43.436 200.557 1.00 50.00 S ATOM 6671 SG CYS 3 259 109.787 37.373 200.872 1.00 50.00 S ATOM 5085 SG CYS 3 34 110.237 65.190 215.142 1.00 50.00 S ATOM 5163 SG CYS 3 45 112.042 68.209 213.331 1.00 50.00 S ATOM 5188 SG CYS 3 48 106.522 69.811 213.756 1.00 50.00 S ATOM 5320 SG CYS 3 83 106.083 67.183 214.984 1.00 50.00 S ATOM 16119 SG CYS 6 111 125.549 73.176 167.027 1.00 50.00 S ATOM 15614 SG CYS 6 46 130.127 75.855 164.202 1.00 50.00 S ATOM 15608 SG CYS 6 45 125.811 79.188 165.859 1.00 50.00 S ATOM 16328 SG CYS 6 140 128.893 76.622 170.582 1.00 50.00 S ATOM 17432 SG CYS 9 101 128.717 75.342 178.757 1.00 50.00 S ATOM 17407 SG CYS 9 98 132.927 71.881 176.396 1.00 50.00 S ATOM 17450 SG CYS 9 104 132.766 73.575 182.746 1.00 50.00 S ATOM 17129 SG CYS 9 63 128.380 69.874 180.032 1.00 50.00 S ATOM 17479 SG CYS 9 108 135.660 72.152 191.041 1.00 50.00 S ATOM 17108 SG CYS 9 59 132.870 68.620 187.221 1.00 50.00 S ATOM 17070 SG CYS 9 53 138.071 66.482 190.851 1.00 50.00 S ATOM 17088 SG CYS 9 56 132.113 68.376 192.922 1.00 50.00 S Time building chain proxies: 19.39, per 1000 atoms: 0.54 Number of scatterers: 36057 At special positions: 0 Unit cell: (177.16, 134.16, 283.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 32 26.01 S 180 16.00 P 1 15.00 O 6221 8.00 N 5998 7.00 C 23625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 2 144 " - pdb=" SG CYS 2 172 " distance=2.05 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.83 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 201 " pdb="FE2 FES 2 201 " - pdb=" SG CYS 2 128 " pdb="FE2 FES 2 201 " - pdb=" SG CYS 2 124 " pdb="FE1 FES 2 201 " - pdb=" SG CYS 2 83 " pdb="FE1 FES 2 201 " - pdb=" SG CYS 2 88 " pdb=" FES 3 804 " pdb="FE2 FES 3 804 " - pdb=" SG CYS 3 48 " pdb="FE2 FES 3 804 " - pdb=" SG CYS 3 83 " pdb="FE1 FES 3 804 " - pdb=" SG CYS 3 34 " pdb="FE1 FES 3 804 " - pdb=" SG CYS 3 45 " pdb=" SF4 1 501 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 353 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 400 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 356 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 115 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 122 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 119 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 128 " pdb=" SF4 3 802 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 181 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 230 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 187 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 184 " pdb=" SF4 3 803 " pdb="FE4 SF4 3 803 " - pdb=" SG CYS 3 259 " pdb="FE2 SF4 3 803 " - pdb=" SG CYS 3 291 " pdb="FE3 SF4 3 803 " - pdb=" SG CYS 3 263 " pdb="FE1 SF4 3 803 " - pdb=" SG CYS 3 256 " pdb=" SF4 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 140 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 46 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 45 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 111 " pdb=" SF4 9 201 " pdb="FE4 SF4 9 201 " - pdb=" SG CYS 9 63 " pdb="FE3 SF4 9 201 " - pdb=" SG CYS 9 104 " pdb="FE2 SF4 9 201 " - pdb=" SG CYS 9 98 " pdb="FE1 SF4 9 201 " - pdb=" SG CYS 9 101 " pdb="FE3 SF4 9 201 " - pdb=" NE2 HIS 9 41 " pdb=" SF4 9 202 " pdb="FE3 SF4 9 202 " - pdb=" SG CYS 9 53 " pdb="FE4 SF4 9 202 " - pdb=" SG CYS 9 56 " pdb="FE2 SF4 9 202 " - pdb=" SG CYS 9 59 " pdb="FE1 SF4 9 202 " - pdb=" SG CYS 9 108 " Number of angles added : 93 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8414 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 186 helices and 22 sheets defined 52.3% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.03 Creating SS restraints... Processing helix chain '1' and resid 29 through 35 Processing helix chain '1' and resid 39 through 47 Processing helix chain '1' and resid 50 through 60 removed outlier: 3.831A pdb=" N VAL 1 57 " --> pdb=" O VAL 1 53 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG 1 59 " --> pdb=" O GLU 1 55 " (cutoff:3.500A) Processing helix chain '1' and resid 72 through 77 Processing helix chain '1' and resid 102 through 109 removed outlier: 4.178A pdb=" N ILE 1 106 " --> pdb=" O LYS 1 102 " (cutoff:3.500A) Processing helix chain '1' and resid 111 through 124 Processing helix chain '1' and resid 140 through 155 Processing helix chain '1' and resid 180 through 183 Processing helix chain '1' and resid 185 through 193 removed outlier: 3.888A pdb=" N MET 1 189 " --> pdb=" O GLU 1 185 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN 1 190 " --> pdb=" O THR 1 186 " (cutoff:3.500A) Processing helix chain '1' and resid 211 through 213 No H-bonds generated for 'chain '1' and resid 211 through 213' Processing helix chain '1' and resid 221 through 233 removed outlier: 4.191A pdb=" N VAL 1 228 " --> pdb=" O LEU 1 224 " (cutoff:3.500A) Proline residue: 1 229 - end of helix Processing helix chain '1' and resid 235 through 239 Processing helix chain '1' and resid 272 through 277 Processing helix chain '1' and resid 304 through 307 No H-bonds generated for 'chain '1' and resid 304 through 307' Processing helix chain '1' and resid 317 through 319 No H-bonds generated for 'chain '1' and resid 317 through 319' Processing helix chain '1' and resid 337 through 350 removed outlier: 3.573A pdb=" N ASN 1 343 " --> pdb=" O ASP 1 339 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS 1 350 " --> pdb=" O ARG 1 346 " (cutoff:3.500A) Processing helix chain '1' and resid 357 through 365 removed outlier: 3.778A pdb=" N VAL 1 363 " --> pdb=" O CYS 1 359 " (cutoff:3.500A) Processing helix chain '1' and resid 367 through 376 Processing helix chain '1' and resid 381 through 397 Proline residue: 1 392 - end of helix removed outlier: 4.290A pdb=" N GLY 1 396 " --> pdb=" O PRO 1 392 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ARG 1 397 " --> pdb=" O LEU 1 393 " (cutoff:3.500A) Processing helix chain '1' and resid 402 through 416 Proline residue: 1 409 - end of helix removed outlier: 3.521A pdb=" N LEU 1 414 " --> pdb=" O VAL 1 410 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG 1 415 " --> pdb=" O LYS 1 411 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS 1 416 " --> pdb=" O GLY 1 412 " (cutoff:3.500A) Processing helix chain '1' and resid 418 through 426 Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 23 through 38 Proline residue: 2 29 - end of helix removed outlier: 3.648A pdb=" N GLN 2 36 " --> pdb=" O ARG 2 33 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU 2 37 " --> pdb=" O VAL 2 34 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU 2 38 " --> pdb=" O GLN 2 35 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 53 Processing helix chain '2' and resid 57 through 66 removed outlier: 3.605A pdb=" N PHE 2 66 " --> pdb=" O GLY 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 86 through 90 Processing helix chain '2' and resid 93 through 104 Processing helix chain '2' and resid 128 through 130 No H-bonds generated for 'chain '2' and resid 128 through 130' Processing helix chain '2' and resid 147 through 158 Processing helix chain '3' and resid 19 through 26 Processing helix chain '3' and resid 98 through 114 removed outlier: 5.006A pdb=" N ASN 3 114 " --> pdb=" O PHE 3 110 " (cutoff:3.500A) Processing helix chain '3' and resid 129 through 137 Processing helix chain '3' and resid 186 through 193 Processing helix chain '3' and resid 206 through 208 No H-bonds generated for 'chain '3' and resid 206 through 208' Processing helix chain '3' and resid 223 through 229 removed outlier: 3.863A pdb=" N ILE 3 226 " --> pdb=" O SER 3 223 " (cutoff:3.500A) Processing helix chain '3' and resid 238 through 240 No H-bonds generated for 'chain '3' and resid 238 through 240' Processing helix chain '3' and resid 246 through 248 No H-bonds generated for 'chain '3' and resid 246 through 248' Processing helix chain '3' and resid 292 through 295 No H-bonds generated for 'chain '3' and resid 292 through 295' Processing helix chain '3' and resid 322 through 333 removed outlier: 4.153A pdb=" N LEU 3 333 " --> pdb=" O LEU 3 329 " (cutoff:3.500A) Processing helix chain '3' and resid 351 through 363 Processing helix chain '3' and resid 402 through 405 No H-bonds generated for 'chain '3' and resid 402 through 405' Processing helix chain '3' and resid 407 through 417 removed outlier: 3.636A pdb=" N VAL 3 417 " --> pdb=" O SER 3 414 " (cutoff:3.500A) Processing helix chain '3' and resid 458 through 461 Processing helix chain '3' and resid 473 through 481 Processing helix chain '3' and resid 488 through 499 Processing helix chain '3' and resid 515 through 527 removed outlier: 4.154A pdb=" N GLU 3 526 " --> pdb=" O ARG 3 522 " (cutoff:3.500A) Processing helix chain '3' and resid 541 through 546 Processing helix chain '3' and resid 574 through 577 No H-bonds generated for 'chain '3' and resid 574 through 577' Processing helix chain '3' and resid 607 through 609 No H-bonds generated for 'chain '3' and resid 607 through 609' Processing helix chain '3' and resid 637 through 648 Processing helix chain '3' and resid 657 through 667 removed outlier: 3.577A pdb=" N GLN 3 661 " --> pdb=" O HIS 3 657 " (cutoff:3.500A) Processing helix chain '3' and resid 701 through 703 No H-bonds generated for 'chain '3' and resid 701 through 703' Processing helix chain '3' and resid 708 through 711 No H-bonds generated for 'chain '3' and resid 708 through 711' Processing helix chain '3' and resid 720 through 725 Processing helix chain '4' and resid 66 through 72 removed outlier: 4.486A pdb=" N GLU 4 71 " --> pdb=" O GLU 4 67 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N HIS 4 72 " --> pdb=" O LYS 4 68 " (cutoff:3.500A) Processing helix chain '4' and resid 75 through 80 removed outlier: 3.721A pdb=" N ILE 4 79 " --> pdb=" O TYR 4 75 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR 4 80 " --> pdb=" O LEU 4 76 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 75 through 80' Processing helix chain '4' and resid 82 through 84 No H-bonds generated for 'chain '4' and resid 82 through 84' Processing helix chain '4' and resid 90 through 105 removed outlier: 3.654A pdb=" N ASP 4 94 " --> pdb=" O SER 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 139 Processing helix chain '4' and resid 143 through 164 removed outlier: 3.575A pdb=" N TYR 4 148 " --> pdb=" O PRO 4 145 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU 4 152 " --> pdb=" O ALA 4 149 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR 4 164 " --> pdb=" O GLU 4 161 " (cutoff:3.500A) Processing helix chain '4' and resid 184 through 208 removed outlier: 3.676A pdb=" N VAL 4 187 " --> pdb=" O GLU 4 184 " (cutoff:3.500A) Proline residue: 4 188 - end of helix removed outlier: 3.587A pdb=" N VAL 4 196 " --> pdb=" O LEU 4 193 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU 4 197 " --> pdb=" O LEU 4 194 " (cutoff:3.500A) Proline residue: 4 198 - end of helix removed outlier: 3.643A pdb=" N ILE 4 201 " --> pdb=" O PRO 4 198 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP 4 202 " --> pdb=" O HIS 4 199 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA 4 206 " --> pdb=" O GLU 4 203 " (cutoff:3.500A) Processing helix chain '4' and resid 212 through 218 removed outlier: 3.822A pdb=" N GLU 4 216 " --> pdb=" O PRO 4 212 " (cutoff:3.500A) Processing helix chain '4' and resid 226 through 231 Processing helix chain '4' and resid 240 through 242 No H-bonds generated for 'chain '4' and resid 240 through 242' Processing helix chain '4' and resid 248 through 251 No H-bonds generated for 'chain '4' and resid 248 through 251' Processing helix chain '4' and resid 257 through 259 No H-bonds generated for 'chain '4' and resid 257 through 259' Processing helix chain '4' and resid 272 through 296 removed outlier: 3.520A pdb=" N ARG 4 279 " --> pdb=" O ARG 4 275 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE 4 280 " --> pdb=" O MET 4 276 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG 4 284 " --> pdb=" O ILE 4 280 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU 4 295 " --> pdb=" O LYS 4 291 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG 4 296 " --> pdb=" O GLN 4 292 " (cutoff:3.500A) Processing helix chain '4' and resid 321 through 332 Processing helix chain '4' and resid 373 through 377 Processing helix chain '4' and resid 379 through 384 removed outlier: 4.477A pdb=" N TYR 4 383 " --> pdb=" O GLN 4 379 " (cutoff:3.500A) Processing helix chain '4' and resid 390 through 400 removed outlier: 4.145A pdb=" N VAL 4 394 " --> pdb=" O VAL 4 390 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA 4 395 " --> pdb=" O PRO 4 391 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE 4 397 " --> pdb=" O MET 4 393 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU 4 400 " --> pdb=" O ILE 4 396 " (cutoff:3.500A) Processing helix chain '4' and resid 404 through 408 Processing helix chain '5' and resid 2 through 13 removed outlier: 4.495A pdb=" N GLU 5 9 " --> pdb=" O ARG 5 5 " (cutoff:3.500A) Processing helix chain '5' and resid 34 through 44 Processing helix chain '5' and resid 111 through 121 Processing helix chain '5' and resid 167 through 169 No H-bonds generated for 'chain '5' and resid 167 through 169' Processing helix chain '5' and resid 187 through 190 Processing helix chain '6' and resid 22 through 35 removed outlier: 3.564A pdb=" N SER 6 35 " --> pdb=" O GLY 6 31 " (cutoff:3.500A) Processing helix chain '6' and resid 45 through 52 removed outlier: 3.731A pdb=" N GLU 6 49 " --> pdb=" O CYS 6 45 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 98 Proline residue: 6 90 - end of helix removed outlier: 3.774A pdb=" N ARG 6 93 " --> pdb=" O PRO 6 90 " (cutoff:3.500A) Processing helix chain '6' and resid 110 through 113 No H-bonds generated for 'chain '6' and resid 110 through 113' Processing helix chain '6' and resid 127 through 129 No H-bonds generated for 'chain '6' and resid 127 through 129' Processing helix chain '6' and resid 144 through 158 Processing helix chain '9' and resid 3 through 18 removed outlier: 3.573A pdb=" N LEU 9 6 " --> pdb=" O LEU 9 3 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER 9 9 " --> pdb=" O LEU 9 6 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU 9 14 " --> pdb=" O GLY 9 11 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE 9 18 " --> pdb=" O LYS 9 15 " (cutoff:3.500A) Processing helix chain '9' and resid 58 through 62 Processing helix chain '9' and resid 103 through 107 Processing helix chain '9' and resid 126 through 129 Processing helix chain '9' and resid 133 through 135 No H-bonds generated for 'chain '9' and resid 133 through 135' Processing helix chain '9' and resid 144 through 152 removed outlier: 3.612A pdb=" N ARG 9 152 " --> pdb=" O ARG 9 148 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 27 removed outlier: 3.635A pdb=" N TYR 7 10 " --> pdb=" O ARG 7 7 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR 7 23 " --> pdb=" O MET 7 20 " (cutoff:3.500A) Processing helix chain '7' and resid 38 through 41 No H-bonds generated for 'chain '7' and resid 38 through 41' Processing helix chain '7' and resid 112 through 126 Processing helix chain 'A' and resid 5 through 30 removed outlier: 3.605A pdb=" N GLY A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 83 removed outlier: 3.763A pdb=" N VAL A 64 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 67 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 71 " --> pdb=" O PHE A 68 " (cutoff:3.500A) Proline residue: A 80 - end of helix removed outlier: 3.821A pdb=" N VAL A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 113 Processing helix chain 'J' and resid 2 through 21 removed outlier: 4.038A pdb=" N LEU J 7 " --> pdb=" O LEU J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 73 Processing helix chain 'J' and resid 88 through 109 Proline residue: J 91 - end of helix removed outlier: 3.617A pdb=" N ALA J 97 " --> pdb=" O ALA J 94 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL J 100 " --> pdb=" O ALA J 97 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE J 103 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 122 No H-bonds generated for 'chain 'J' and resid 120 through 122' Processing helix chain 'J' and resid 124 through 131 Proline residue: J 129 - end of helix Processing helix chain 'J' and resid 136 through 157 Processing helix chain 'K' and resid 2 through 20 removed outlier: 3.760A pdb=" N ALA K 8 " --> pdb=" O LEU K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 49 removed outlier: 3.562A pdb=" N LEU K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA K 48 " --> pdb=" O GLY K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 79 Processing helix chain 'K' and resid 87 through 89 No H-bonds generated for 'chain 'K' and resid 87 through 89' Processing helix chain 'L' and resid 2 through 19 removed outlier: 3.714A pdb=" N THR L 6 " --> pdb=" O ALA L 2 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE L 7 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Proline residue: L 10 - end of helix removed outlier: 4.293A pdb=" N PHE L 14 " --> pdb=" O PRO L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 49 removed outlier: 3.506A pdb=" N SER L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE L 41 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU L 47 " --> pdb=" O LEU L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 94 Processing helix chain 'L' and resid 101 through 119 Processing helix chain 'L' and resid 124 through 142 Processing helix chain 'L' and resid 150 through 178 removed outlier: 5.498A pdb=" N ALA L 155 " --> pdb=" O TYR L 151 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG L 163 " --> pdb=" O PHE L 159 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY L 165 " --> pdb=" O VAL L 161 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP L 177 " --> pdb=" O MET L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 192 Processing helix chain 'L' and resid 199 through 216 removed outlier: 3.514A pdb=" N GLY L 215 " --> pdb=" O LEU L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 230 Processing helix chain 'L' and resid 234 through 241 Processing helix chain 'L' and resid 246 through 262 removed outlier: 4.038A pdb=" N VAL L 250 " --> pdb=" O VAL L 246 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE L 253 " --> pdb=" O GLY L 249 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE L 258 " --> pdb=" O ALA L 254 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU L 259 " --> pdb=" O ARG L 255 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL L 262 " --> pdb=" O PHE L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 284 Processing helix chain 'L' and resid 291 through 312 removed outlier: 3.871A pdb=" N SER L 298 " --> pdb=" O ILE L 294 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL L 312 " --> pdb=" O LEU L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 342 removed outlier: 3.931A pdb=" N PHE L 327 " --> pdb=" O PHE L 323 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA L 330 " --> pdb=" O ALA L 326 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER L 338 " --> pdb=" O LEU L 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 374 Processing helix chain 'L' and resid 380 through 394 removed outlier: 3.959A pdb=" N LEU L 393 " --> pdb=" O LEU L 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 425 removed outlier: 3.679A pdb=" N VAL L 404 " --> pdb=" O VAL L 400 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY L 405 " --> pdb=" O GLY L 401 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU L 408 " --> pdb=" O VAL L 404 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA L 417 " --> pdb=" O THR L 413 " (cutoff:3.500A) Processing helix chain 'L' and resid 440 through 455 Proline residue: L 445 - end of helix Processing helix chain 'L' and resid 470 through 474 Processing helix chain 'L' and resid 491 through 511 removed outlier: 3.919A pdb=" N GLY L 508 " --> pdb=" O GLY L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 529 removed outlier: 3.713A pdb=" N ALA L 523 " --> pdb=" O ALA L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 531 through 541 removed outlier: 6.123A pdb=" N ASP L 535 " --> pdb=" O PHE L 532 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG L 536 " --> pdb=" O TYR L 533 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU L 541 " --> pdb=" O TYR L 538 " (cutoff:3.500A) Processing helix chain 'L' and resid 543 through 579 removed outlier: 3.511A pdb=" N GLU L 551 " --> pdb=" O LYS L 547 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU L 567 " --> pdb=" O GLY L 563 " (cutoff:3.500A) Processing helix chain 'L' and resid 586 through 604 Processing helix chain 'M' and resid 2 through 17 Proline residue: M 9 - end of helix removed outlier: 3.511A pdb=" N LEU M 16 " --> pdb=" O PHE M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 41 removed outlier: 3.813A pdb=" N LEU M 27 " --> pdb=" O ALA M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 59 No H-bonds generated for 'chain 'M' and resid 57 through 59' Processing helix chain 'M' and resid 71 through 88 removed outlier: 3.617A pdb=" N LEU M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 111 Processing helix chain 'M' and resid 115 through 134 removed outlier: 4.248A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 141 through 168 Proline residue: M 158 - end of helix removed outlier: 4.446A pdb=" N ALA M 161 " --> pdb=" O LEU M 157 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA M 162 " --> pdb=" O PRO M 158 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG M 167 " --> pdb=" O VAL M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 202 removed outlier: 4.042A pdb=" N ALA M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 208 through 210 No H-bonds generated for 'chain 'M' and resid 208 through 210' Processing helix chain 'M' and resid 212 through 220 Proline residue: M 216 - end of helix Processing helix chain 'M' and resid 226 through 232 Processing helix chain 'M' and resid 237 through 243 Processing helix chain 'M' and resid 245 through 248 No H-bonds generated for 'chain 'M' and resid 245 through 248' Processing helix chain 'M' and resid 250 through 277 removed outlier: 4.397A pdb=" N GLN M 255 " --> pdb=" O GLU M 251 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLY M 258 " --> pdb=" O ALA M 254 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU M 259 " --> pdb=" O GLN M 255 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE M 276 " --> pdb=" O ALA M 272 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA M 277 " --> pdb=" O TRP M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 302 Processing helix chain 'M' and resid 305 through 336 removed outlier: 3.616A pdb=" N MET M 309 " --> pdb=" O PRO M 305 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU M 312 " --> pdb=" O ALA M 308 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY M 319 " --> pdb=" O LEU M 315 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL M 320 " --> pdb=" O ALA M 316 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU M 325 " --> pdb=" O TYR M 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 354 through 366 Processing helix chain 'M' and resid 372 through 387 removed outlier: 4.450A pdb=" N GLY M 376 " --> pdb=" O SER M 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 389 through 414 removed outlier: 3.563A pdb=" N LEU M 397 " --> pdb=" O ALA M 393 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER M 398 " --> pdb=" O LEU M 394 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL M 399 " --> pdb=" O ALA M 395 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE M 400 " --> pdb=" O PHE M 396 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA M 401 " --> pdb=" O LEU M 397 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR M 413 " --> pdb=" O ALA M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 427 through 445 removed outlier: 3.868A pdb=" N GLY M 431 " --> pdb=" O GLY M 427 " (cutoff:3.500A) Processing helix chain 'M' and resid 447 through 449 No H-bonds generated for 'chain 'M' and resid 447 through 449' Processing helix chain 'M' and resid 452 through 465 Proline residue: M 456 - end of helix removed outlier: 5.208A pdb=" N LEU M 465 " --> pdb=" O PHE M 461 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 18 removed outlier: 3.951A pdb=" N LEU N 15 " --> pdb=" O VAL N 11 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N PHE N 18 " --> pdb=" O THR N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 43 Processing helix chain 'N' and resid 57 through 76 removed outlier: 3.575A pdb=" N VAL N 74 " --> pdb=" O ALA N 70 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU N 76 " --> pdb=" O TRP N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 99 removed outlier: 5.572A pdb=" N LEU N 87 " --> pdb=" O PHE N 84 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR N 90 " --> pdb=" O LEU N 87 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU N 97 " --> pdb=" O GLY N 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 122 Proline residue: N 117 - end of helix removed outlier: 3.560A pdb=" N ALA N 120 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 157 removed outlier: 3.808A pdb=" N ALA N 133 " --> pdb=" O GLY N 129 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY N 156 " --> pdb=" O ALA N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 170 through 187 removed outlier: 3.567A pdb=" N LEU N 180 " --> pdb=" O LEU N 176 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL N 181 " --> pdb=" O GLY N 177 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY N 182 " --> pdb=" O LEU N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 193 through 202 Proline residue: N 197 - end of helix removed outlier: 3.873A pdb=" N TYR N 200 " --> pdb=" O PRO N 197 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 225 removed outlier: 4.958A pdb=" N LYS N 216 " --> pdb=" O ALA N 212 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG N 225 " --> pdb=" O ALA N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 230 through 250 removed outlier: 3.626A pdb=" N ALA N 234 " --> pdb=" O PRO N 230 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU N 249 " --> pdb=" O ASN N 245 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA N 250 " --> pdb=" O LEU N 246 " (cutoff:3.500A) Processing helix chain 'N' and resid 254 through 272 removed outlier: 3.996A pdb=" N ALA N 266 " --> pdb=" O SER N 262 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU N 271 " --> pdb=" O GLY N 267 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA N 272 " --> pdb=" O TYR N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 280 through 302 Processing helix chain 'N' and resid 309 through 312 Processing helix chain 'N' and resid 315 through 318 No H-bonds generated for 'chain 'N' and resid 315 through 318' Processing helix chain 'N' and resid 320 through 334 Processing helix chain 'N' and resid 340 through 355 removed outlier: 3.574A pdb=" N ALA N 348 " --> pdb=" O GLY N 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 359 through 379 removed outlier: 3.523A pdb=" N VAL N 370 " --> pdb=" O VAL N 366 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR N 373 " --> pdb=" O ALA N 369 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR N 374 " --> pdb=" O VAL N 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 381 through 383 No H-bonds generated for 'chain 'N' and resid 381 through 383' Processing helix chain 'N' and resid 396 through 414 Processing helix chain 'N' and resid 416 through 422 Proline residue: N 421 - end of helix Processing helix chain 'H' and resid 10 through 42 removed outlier: 3.515A pdb=" N PHE H 42 " --> pdb=" O LEU H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 66 Processing helix chain 'H' and resid 79 through 94 removed outlier: 3.515A pdb=" N VAL H 83 " --> pdb=" O ARG H 79 " (cutoff:3.500A) Proline residue: H 86 - end of helix removed outlier: 3.661A pdb=" N ALA H 93 " --> pdb=" O SER H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 143 removed outlier: 3.538A pdb=" N LEU H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA H 132 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL H 133 " --> pdb=" O SER H 129 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY H 135 " --> pdb=" O LEU H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 177 removed outlier: 3.565A pdb=" N LEU H 164 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY H 165 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY H 167 " --> pdb=" O GLU H 163 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU H 168 " --> pdb=" O LEU H 164 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU H 171 " --> pdb=" O GLY H 167 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA H 172 " --> pdb=" O LEU H 168 " (cutoff:3.500A) Proline residue: H 173 - end of helix removed outlier: 4.010A pdb=" N LEU H 176 " --> pdb=" O ALA H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 191 removed outlier: 3.515A pdb=" N GLU H 191 " --> pdb=" O ASN H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 211 Processing helix chain 'H' and resid 239 through 263 removed outlier: 3.548A pdb=" N TYR H 249 " --> pdb=" O GLN H 245 " (cutoff:3.500A) Proline residue: H 260 - end of helix Processing helix chain 'H' and resid 277 through 296 Processing helix chain 'H' and resid 302 through 311 Processing helix chain 'H' and resid 313 through 329 Processing helix chain 'H' and resid 335 through 350 removed outlier: 4.000A pdb=" N LEU H 340 " --> pdb=" O TYR H 336 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '1' and resid 215 through 220 removed outlier: 3.657A pdb=" N TYR 1 88 " --> pdb=" O PRO 1 215 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL 1 129 " --> pdb=" O LEU 1 89 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N CYS 1 91 " --> pdb=" O VAL 1 129 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR 1 131 " --> pdb=" O CYS 1 91 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA 1 93 " --> pdb=" O TYR 1 131 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR 1 133 " --> pdb=" O ALA 1 93 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP 1 170 " --> pdb=" O GLY 1 130 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE 1 132 " --> pdb=" O ASP 1 170 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N HIS 1 172 " --> pdb=" O ILE 1 132 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL 1 134 " --> pdb=" O HIS 1 172 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS 1 174 " --> pdb=" O VAL 1 134 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 249 through 254 removed outlier: 3.692A pdb=" N TYR 1 252 " --> pdb=" O TYR 1 264 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY 1 262 " --> pdb=" O ILE 1 254 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '1' and resid 287 through 291 removed outlier: 6.886A pdb=" N ILE 1 331 " --> pdb=" O GLN 1 288 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE 1 290 " --> pdb=" O ILE 1 329 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE 1 329 " --> pdb=" O ILE 1 290 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 117 through 122 removed outlier: 5.967A pdb=" N TYR 2 78 " --> pdb=" O SER 2 118 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLN 2 120 " --> pdb=" O TYR 2 78 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU 2 80 " --> pdb=" O GLN 2 120 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL 2 122 " --> pdb=" O LEU 2 80 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL 2 82 " --> pdb=" O VAL 2 122 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 9 through 11 removed outlier: 5.722A pdb=" N MET 3 91 " --> pdb=" O LYS 3 5 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 235 through 237 removed outlier: 3.711A pdb=" N SER 3 171 " --> pdb=" O VAL 3 174 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU 3 176 " --> pdb=" O PRO 3 169 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 250 through 255 removed outlier: 6.817A pdb=" N ARG 3 270 " --> pdb=" O LEU 3 274 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU 3 274 " --> pdb=" O ARG 3 270 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '3' and resid 310 through 312 Processing sheet with id= I, first strand: chain '3' and resid 369 through 371 removed outlier: 8.146A pdb=" N ASP 3 370 " --> pdb=" O VAL 3 341 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU 3 343 " --> pdb=" O ASP 3 370 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR 3 565 " --> pdb=" O GLY 3 342 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR 3 344 " --> pdb=" O TYR 3 565 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR 3 567 " --> pdb=" O TYR 3 344 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE 3 582 " --> pdb=" O ALA 3 566 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N TYR 3 568 " --> pdb=" O PHE 3 582 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL 3 584 " --> pdb=" O TYR 3 568 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL 3 600 " --> pdb=" O MET 3 585 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU 3 587 " --> pdb=" O VAL 3 600 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU 3 602 " --> pdb=" O LEU 3 587 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '3' and resid 464 through 467 removed outlier: 4.501A pdb=" N ILE 3 464 " --> pdb=" O MET 3 448 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA 3 452 " --> pdb=" O GLU 3 466 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA 3 396 " --> pdb=" O ALA 3 449 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE 3 451 " --> pdb=" O ALA 3 396 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL 3 398 " --> pdb=" O PHE 3 451 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS 3 531 " --> pdb=" O LEU 3 505 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU 3 507 " --> pdb=" O LYS 3 531 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU 3 533 " --> pdb=" O LEU 3 507 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 612 through 615 Processing sheet with id= L, first strand: chain '3' and resid 692 through 696 removed outlier: 5.483A pdb=" N LEU 3 758 " --> pdb=" O TYR 3 693 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ARG 3 695 " --> pdb=" O LEU 3 758 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU 3 760 " --> pdb=" O ARG 3 695 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain '3' and resid 714 through 718 removed outlier: 4.271A pdb=" N ALA 3 714 " --> pdb=" O GLU 3 744 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '4' and resid 27 through 30 Processing sheet with id= O, first strand: chain '4' and resid 339 through 348 removed outlier: 4.173A pdb=" N VAL 4 344 " --> pdb=" O TYR 4 355 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR 4 355 " --> pdb=" O VAL 4 344 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '5' and resid 52 through 56 removed outlier: 3.554A pdb=" N PHE 5 68 " --> pdb=" O VAL 5 94 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '6' and resid 38 through 42 removed outlier: 5.613A pdb=" N VAL 6 77 " --> pdb=" O ALA 6 39 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE 6 41 " --> pdb=" O VAL 6 77 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE 6 79 " --> pdb=" O PHE 6 41 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP 6 104 " --> pdb=" O MET 6 78 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL 6 80 " --> pdb=" O TRP 6 104 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE 6 106 " --> pdb=" O VAL 6 80 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL 6 135 " --> pdb=" O SER 6 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain '9' and resid 31 through 33 Processing sheet with id= S, first strand: chain '9' and resid 130 through 132 removed outlier: 3.548A pdb=" N LYS 9 89 " --> pdb=" O GLU 9 71 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU 9 71 " --> pdb=" O LYS 9 89 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR 9 91 " --> pdb=" O TYR 9 69 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR 9 69 " --> pdb=" O TYR 9 91 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '7' and resid 102 through 105 removed outlier: 4.168A pdb=" N ILE 7 91 " --> pdb=" O LEU 7 86 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU 7 59 " --> pdb=" O PHE 7 67 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU 7 69 " --> pdb=" O ALA 7 57 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA 7 57 " --> pdb=" O LEU 7 69 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR 7 56 " --> pdb=" O ALA 7 35 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER 7 58 " --> pdb=" O LYS 7 33 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LYS 7 33 " --> pdb=" O SER 7 58 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER 7 60 " --> pdb=" O PHE 7 31 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N PHE 7 31 " --> pdb=" O SER 7 60 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 53 through 58 Processing sheet with id= V, first strand: chain 'M' and resid 51 through 56 removed outlier: 7.119A pdb=" N VAL M 61 " --> pdb=" O LEU M 55 " (cutoff:3.500A) 1597 hydrogen bonds defined for protein. 4353 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: 11.79 Time building geometry restraints manager: 15.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.44: 18531 1.44 - 1.67: 18173 1.67 - 1.90: 256 1.90 - 2.13: 1 2.13 - 2.36: 91 Bond restraints: 37052 Sorted by residual: bond pdb=" CD GLU H 227 " pdb=" OE2 GLU H 227 " ideal model delta sigma weight residual 1.249 1.395 -0.146 1.90e-02 2.77e+03 5.93e+01 bond pdb=" CD GLU 9 92 " pdb=" OE1 GLU 9 92 " ideal model delta sigma weight residual 1.249 1.394 -0.145 1.90e-02 2.77e+03 5.86e+01 bond pdb=" CG ASP L 386 " pdb=" OD2 ASP L 386 " ideal model delta sigma weight residual 1.249 1.394 -0.145 1.90e-02 2.77e+03 5.84e+01 bond pdb=" CD GLU A 110 " pdb=" OE2 GLU A 110 " ideal model delta sigma weight residual 1.249 1.393 -0.144 1.90e-02 2.77e+03 5.78e+01 bond pdb=" CD GLU 3 415 " pdb=" OE2 GLU 3 415 " ideal model delta sigma weight residual 1.249 1.393 -0.144 1.90e-02 2.77e+03 5.74e+01 ... (remaining 37047 not shown) Histogram of bond angle deviations from ideal: 60.45 - 75.13: 87 75.13 - 89.80: 1 89.80 - 104.48: 1289 104.48 - 119.16: 29326 119.16 - 133.84: 19761 Bond angle restraints: 50464 Sorted by residual: angle pdb=" S1 FES 3 804 " pdb="FE2 FES 3 804 " pdb=" S2 FES 3 804 " ideal model delta sigma weight residual 104.33 117.80 -13.47 1.14e+00 7.69e-01 1.40e+02 angle pdb="FE1 FES 3 804 " pdb=" S2 FES 3 804 " pdb="FE2 FES 3 804 " ideal model delta sigma weight residual 75.66 63.13 12.53 1.14e+00 7.69e-01 1.21e+02 angle pdb="FE1 FES 3 804 " pdb=" S1 FES 3 804 " pdb="FE2 FES 3 804 " ideal model delta sigma weight residual 75.66 63.87 11.79 1.20e+00 6.94e-01 9.65e+01 angle pdb=" CA PRO M 215 " pdb=" C PRO M 215 " pdb=" N PRO M 216 " ideal model delta sigma weight residual 117.93 129.27 -11.34 1.20e+00 6.94e-01 8.94e+01 angle pdb=" CA PRO 4 337 " pdb=" C PRO 4 337 " pdb=" N PRO 4 338 " ideal model delta sigma weight residual 117.93 129.14 -11.21 1.20e+00 6.94e-01 8.72e+01 ... (remaining 50459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.94: 20963 31.94 - 63.88: 564 63.88 - 95.82: 117 95.82 - 127.76: 0 127.76 - 159.69: 1 Dihedral angle restraints: 21645 sinusoidal: 8418 harmonic: 13227 Sorted by residual: dihedral pdb=" CA ALA 4 142 " pdb=" C ALA 4 142 " pdb=" N LEU 4 143 " pdb=" CA LEU 4 143 " ideal model delta harmonic sigma weight residual -180.00 -136.91 -43.09 0 5.00e+00 4.00e-02 7.43e+01 dihedral pdb=" CA ASP 6 55 " pdb=" C ASP 6 55 " pdb=" N ALA 6 56 " pdb=" CA ALA 6 56 " ideal model delta harmonic sigma weight residual 180.00 138.51 41.49 0 5.00e+00 4.00e-02 6.88e+01 dihedral pdb=" CA PHE H 219 " pdb=" C PHE H 219 " pdb=" N ASP H 220 " pdb=" CA ASP H 220 " ideal model delta harmonic sigma weight residual 180.00 139.60 40.40 0 5.00e+00 4.00e-02 6.53e+01 ... (remaining 21642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.193: 5636 4.193 - 8.386: 0 8.386 - 12.579: 0 12.579 - 16.771: 0 16.771 - 20.964: 28 Chirality restraints: 5664 Sorted by residual: chirality pdb="FE3 SF4 3 801 " pdb=" S1 SF4 3 801 " pdb=" S2 SF4 3 801 " pdb=" S4 SF4 3 801 " both_signs ideal model delta sigma weight residual False -10.55 10.41 -20.96 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE3 SF4 3 803 " pdb=" S1 SF4 3 803 " pdb=" S2 SF4 3 803 " pdb=" S4 SF4 3 803 " both_signs ideal model delta sigma weight residual False -10.55 10.40 -20.96 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE3 SF4 1 501 " pdb=" S1 SF4 1 501 " pdb=" S2 SF4 1 501 " pdb=" S4 SF4 1 501 " both_signs ideal model delta sigma weight residual False -10.55 10.12 -20.68 2.00e-01 2.50e+01 1.07e+04 ... (remaining 5661 not shown) Planarity restraints: 6374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 316 " -0.373 2.00e-02 2.50e+03 2.00e-01 7.98e+02 pdb=" CG TYR N 316 " 0.107 2.00e-02 2.50e+03 pdb=" CD1 TYR N 316 " 0.181 2.00e-02 2.50e+03 pdb=" CD2 TYR N 316 " 0.172 2.00e-02 2.50e+03 pdb=" CE1 TYR N 316 " 0.105 2.00e-02 2.50e+03 pdb=" CE2 TYR N 316 " 0.100 2.00e-02 2.50e+03 pdb=" CZ TYR N 316 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR N 316 " -0.292 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 4 257 " -0.256 2.00e-02 2.50e+03 1.39e-01 3.86e+02 pdb=" CG TYR 4 257 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR 4 257 " 0.102 2.00e-02 2.50e+03 pdb=" CD2 TYR 4 257 " 0.129 2.00e-02 2.50e+03 pdb=" CE1 TYR 4 257 " 0.077 2.00e-02 2.50e+03 pdb=" CE2 TYR 4 257 " 0.071 2.00e-02 2.50e+03 pdb=" CZ TYR 4 257 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR 4 257 " -0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 344 " 0.258 2.00e-02 2.50e+03 1.36e-01 3.71e+02 pdb=" CG TYR M 344 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 TYR M 344 " -0.117 2.00e-02 2.50e+03 pdb=" CD2 TYR M 344 " -0.117 2.00e-02 2.50e+03 pdb=" CE1 TYR M 344 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR M 344 " -0.070 2.00e-02 2.50e+03 pdb=" CZ TYR M 344 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR M 344 " 0.193 2.00e-02 2.50e+03 ... (remaining 6371 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1949 2.71 - 3.26: 37279 3.26 - 3.80: 57836 3.80 - 4.35: 74207 4.35 - 4.90: 121655 Nonbonded interactions: 292926 Sorted by model distance: nonbonded pdb=" O2P FMN 1 502 " pdb=" O4' FMN 1 502 " model vdw 2.162 2.440 nonbonded pdb=" CB ASN 1 220 " pdb=" O2P FMN 1 502 " model vdw 2.261 3.440 nonbonded pdb=" N SER H 179 " pdb=" O SER H 179 " model vdw 2.331 2.496 nonbonded pdb=" N ALA 5 173 " pdb=" O ALA 5 173 " model vdw 2.334 2.496 nonbonded pdb=" N MET 1 322 " pdb=" O MET 1 322 " model vdw 2.371 2.496 ... (remaining 292921 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: 5.680 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: 30.820 Check model and map are aligned: 0.470 Set scattering table: 0.350 Process input model: 102.660 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 : 0.021 0.146 37052 Z= 1.383 Angle : 2.330 13.686 50464 Z= 1.560 Chirality : 1.407 20.964 5664 Planarity : 0.023 0.204 6374 Dihedral : 15.365 159.694 13228 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 2.86 % Allowed : 9.56 % Favored : 87.58 % Rotamer: Outliers : 2.43 % Allowed : 6.43 % Favored : 91.14 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.37 % 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: -4.76 (0.10), residues: 4612 helix: -3.11 (0.07), residues: 2460 sheet: -1.95 (0.28), residues: 291 loop : -3.27 (0.12), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.209 0.028 TRP M 213 HIS 0.010 0.002 HIS 4 93 PHE 0.141 0.021 PHE H 314 TYR 0.373 0.034 TYR N 316 ARG 0.013 0.001 ARG M 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1431 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1342 time to evaluate : 4.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 43 ARG cc_start: 0.7597 (mtm110) cc_final: 0.6811 (mtm110) REVERT: 1 79 MET cc_start: 0.8399 (mmm) cc_final: 0.7723 (mmm) REVERT: 1 158 LEU cc_start: 0.8885 (tp) cc_final: 0.8684 (tp) REVERT: 1 189 MET cc_start: 0.7560 (mtm) cc_final: 0.7190 (mtm) REVERT: 1 238 PHE cc_start: 0.8426 (t80) cc_final: 0.7756 (t80) REVERT: 1 253 GLN cc_start: 0.7641 (mp10) cc_final: 0.7087 (pm20) REVERT: 1 408 TRP cc_start: 0.8249 (m-10) cc_final: 0.7887 (m-10) REVERT: 2 43 PRO cc_start: 0.9248 (OUTLIER) cc_final: 0.9027 (Cg_endo) REVERT: 2 81 GLN cc_start: 0.8367 (mt0) cc_final: 0.8071 (mt0) REVERT: 2 141 TYR cc_start: 0.6911 (m-80) cc_final: 0.6607 (m-10) REVERT: 3 1 MET cc_start: 0.8294 (mtt) cc_final: 0.7954 (mtt) REVERT: 3 96 LEU cc_start: 0.8969 (mt) cc_final: 0.8669 (mt) REVERT: 3 133 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8654 (mmp80) REVERT: 3 214 MET cc_start: 0.7965 (tpt) cc_final: 0.6771 (tpt) REVERT: 3 239 THR cc_start: 0.8519 (m) cc_final: 0.7753 (t) REVERT: 3 274 LEU cc_start: 0.8990 (tp) cc_final: 0.8693 (tt) REVERT: 3 288 ILE cc_start: 0.8998 (pt) cc_final: 0.8673 (mt) REVERT: 3 391 LEU cc_start: 0.8889 (mt) cc_final: 0.8624 (mp) REVERT: 3 395 PHE cc_start: 0.8850 (t80) cc_final: 0.8279 (t80) REVERT: 3 494 LYS cc_start: 0.8558 (tttt) cc_final: 0.8283 (ttpp) REVERT: 3 582 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6304 (t80) REVERT: 3 618 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7184 (tt0) REVERT: 3 664 LEU cc_start: 0.8638 (tp) cc_final: 0.8436 (tt) REVERT: 4 68 LYS cc_start: 0.9600 (tptt) cc_final: 0.9142 (tptp) REVERT: 4 93 HIS cc_start: 0.8801 (m90) cc_final: 0.8230 (m-70) REVERT: 4 94 ASP cc_start: 0.8527 (m-30) cc_final: 0.8099 (m-30) REVERT: 4 140 LEU cc_start: 0.8154 (tp) cc_final: 0.7890 (tt) REVERT: 4 160 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8776 (t80) REVERT: 4 184 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: 4 192 LYS cc_start: 0.8607 (mttt) cc_final: 0.8228 (mtmm) REVERT: 4 216 GLU cc_start: 0.5572 (mt-10) cc_final: 0.4976 (mt-10) REVERT: 4 232 LEU cc_start: 0.9241 (mt) cc_final: 0.8995 (mp) REVERT: 4 239 LEU cc_start: 0.9052 (tp) cc_final: 0.8849 (tp) REVERT: 4 268 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6733 (pm20) REVERT: 4 275 ARG cc_start: 0.8229 (mtm-85) cc_final: 0.7850 (mpp80) REVERT: 4 276 MET cc_start: 0.8955 (mmt) cc_final: 0.8531 (tpp) REVERT: 4 283 MET cc_start: 0.8063 (mtp) cc_final: 0.7836 (mtt) REVERT: 4 285 GLU cc_start: 0.6574 (tt0) cc_final: 0.6145 (tp30) REVERT: 4 309 ILE cc_start: 0.9375 (pt) cc_final: 0.9136 (pt) REVERT: 4 344 VAL cc_start: 0.9460 (t) cc_final: 0.9052 (p) REVERT: 4 396 ILE cc_start: 0.9224 (mt) cc_final: 0.8757 (tt) REVERT: 5 17 ILE cc_start: 0.8745 (mm) cc_final: 0.8315 (pt) REVERT: 5 22 LEU cc_start: 0.8983 (mm) cc_final: 0.8626 (mt) REVERT: 5 115 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7665 (mm-30) REVERT: 5 146 LEU cc_start: 0.9351 (mt) cc_final: 0.8930 (mt) REVERT: 5 177 LYS cc_start: 0.8799 (mttt) cc_final: 0.8557 (mttt) REVERT: 6 45 CYS cc_start: 0.9718 (OUTLIER) cc_final: 0.9306 (p) REVERT: 6 59 ASP cc_start: 0.7121 (m-30) cc_final: 0.6862 (m-30) REVERT: 6 78 MET cc_start: 0.9264 (ttm) cc_final: 0.9002 (ttm) REVERT: 6 88 MET cc_start: 0.9041 (tpt) cc_final: 0.8716 (tpt) REVERT: 6 101 ASP cc_start: 0.8278 (t70) cc_final: 0.7698 (t0) REVERT: 6 106 ILE cc_start: 0.9531 (mt) cc_final: 0.9249 (pt) REVERT: 6 108 MET cc_start: 0.9076 (ttt) cc_final: 0.8744 (ttm) REVERT: 6 114 SER cc_start: 0.9253 (m) cc_final: 0.8758 (p) REVERT: 6 134 ASP cc_start: 0.9489 (m-30) cc_final: 0.9204 (m-30) REVERT: 6 157 LYS cc_start: 0.8839 (tttm) cc_final: 0.8637 (tttt) REVERT: 9 44 THR cc_start: 0.9500 (p) cc_final: 0.9173 (p) REVERT: 9 89 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8429 (tttm) REVERT: 9 114 VAL cc_start: 0.9205 (t) cc_final: 0.9002 (p) REVERT: 9 118 ASP cc_start: 0.9196 (m-30) cc_final: 0.8791 (m-30) REVERT: 9 119 PHE cc_start: 0.8890 (p90) cc_final: 0.8252 (p90) REVERT: 9 128 ASP cc_start: 0.8574 (m-30) cc_final: 0.8192 (m-30) REVERT: 9 131 TYR cc_start: 0.8481 (m-80) cc_final: 0.8145 (m-80) REVERT: 9 136 MET cc_start: 0.8748 (mtm) cc_final: 0.8392 (mtt) REVERT: 9 159 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8230 (m) REVERT: 9 170 LEU cc_start: 0.8877 (mt) cc_final: 0.8673 (mt) REVERT: 7 17 LEU cc_start: 0.8911 (mt) cc_final: 0.8678 (tp) REVERT: 7 91 ILE cc_start: 0.8754 (mt) cc_final: 0.8476 (tp) REVERT: 7 97 TYR cc_start: 0.7440 (t80) cc_final: 0.6977 (t80) REVERT: A 11 LEU cc_start: 0.8788 (mt) cc_final: 0.8515 (tt) REVERT: A 56 ARG cc_start: 0.7364 (mpt180) cc_final: 0.6956 (ptp-170) REVERT: A 57 PHE cc_start: 0.8601 (m-80) cc_final: 0.8185 (m-80) REVERT: A 72 ASP cc_start: 0.8035 (t70) cc_final: 0.7763 (t70) REVERT: A 104 PHE cc_start: 0.8710 (t80) cc_final: 0.8426 (t80) REVERT: A 108 LEU cc_start: 0.9066 (mt) cc_final: 0.8419 (tt) REVERT: A 110 GLU cc_start: 0.6848 (pp20) cc_final: 0.6130 (pp20) REVERT: J 20 VAL cc_start: 0.9017 (m) cc_final: 0.8718 (t) REVERT: J 36 PHE cc_start: 0.8909 (m-10) cc_final: 0.8359 (m-10) REVERT: J 55 GLN cc_start: 0.9192 (tp-100) cc_final: 0.8377 (tp40) REVERT: J 59 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7865 (t80) REVERT: J 64 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8154 (t) REVERT: J 65 VAL cc_start: 0.8196 (t) cc_final: 0.7976 (t) REVERT: J 67 PHE cc_start: 0.8190 (m-80) cc_final: 0.7931 (m-10) REVERT: J 139 LEU cc_start: 0.9545 (tp) cc_final: 0.9344 (tp) REVERT: J 140 LEU cc_start: 0.9181 (mt) cc_final: 0.8884 (mm) REVERT: K 19 LEU cc_start: 0.8643 (mt) cc_final: 0.8317 (mt) REVERT: K 28 PHE cc_start: 0.8094 (t80) cc_final: 0.6908 (t80) REVERT: K 36 ASN cc_start: 0.7977 (m110) cc_final: 0.6062 (m110) REVERT: K 80 ARG cc_start: 0.8294 (ttt90) cc_final: 0.8063 (ttp-110) REVERT: L 67 LEU cc_start: 0.8019 (mt) cc_final: 0.7764 (mt) REVERT: L 78 LEU cc_start: 0.8029 (mt) cc_final: 0.7819 (tp) REVERT: L 134 VAL cc_start: 0.7824 (m) cc_final: 0.7546 (t) REVERT: L 153 ASP cc_start: 0.8158 (m-30) cc_final: 0.7762 (t0) REVERT: L 169 PHE cc_start: 0.8045 (t80) cc_final: 0.7365 (t80) REVERT: L 187 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6858 (pp20) REVERT: L 188 LEU cc_start: 0.9275 (tp) cc_final: 0.8657 (tp) REVERT: L 192 MET cc_start: 0.8390 (ttm) cc_final: 0.8137 (mtp) REVERT: L 223 MET cc_start: 0.7177 (pp-130) cc_final: 0.6525 (pp-130) REVERT: L 244 THR cc_start: 0.7441 (p) cc_final: 0.6710 (p) REVERT: L 245 MET cc_start: 0.8316 (tpt) cc_final: 0.7065 (tpt) REVERT: L 261 SER cc_start: 0.8919 (p) cc_final: 0.8558 (m) REVERT: L 293 LYS cc_start: 0.8405 (mttm) cc_final: 0.7754 (mtpt) REVERT: L 334 LEU cc_start: 0.8115 (mt) cc_final: 0.7651 (mt) REVERT: L 463 HIS cc_start: 0.5523 (OUTLIER) cc_final: 0.5036 (t70) REVERT: L 483 HIS cc_start: 0.0532 (OUTLIER) cc_final: -0.0323 (p90) REVERT: M 67 LEU cc_start: 0.9213 (tp) cc_final: 0.8957 (tp) REVERT: M 106 LEU cc_start: 0.9134 (mt) cc_final: 0.8813 (mm) REVERT: M 107 LEU cc_start: 0.9078 (mt) cc_final: 0.8834 (mt) REVERT: M 116 LEU cc_start: 0.6310 (tp) cc_final: 0.5794 (tp) REVERT: M 132 MET cc_start: 0.8406 (ptm) cc_final: 0.7953 (ptp) REVERT: M 135 LEU cc_start: 0.8815 (mt) cc_final: 0.8518 (tp) REVERT: M 183 HIS cc_start: 0.7081 (m-70) cc_final: 0.6336 (m170) REVERT: M 201 PHE cc_start: 0.7975 (m-10) cc_final: 0.7734 (m-10) REVERT: M 251 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7020 (mp0) REVERT: M 386 LYS cc_start: 0.8173 (mttm) cc_final: 0.7766 (mttm) REVERT: M 435 LEU cc_start: 0.9259 (tp) cc_final: 0.8954 (tp) REVERT: N 119 TYR cc_start: 0.9341 (m-80) cc_final: 0.9055 (m-80) REVERT: N 163 LEU cc_start: 0.8107 (mt) cc_final: 0.7455 (mt) REVERT: N 210 PHE cc_start: 0.8082 (t80) cc_final: 0.7068 (t80) REVERT: N 214 SER cc_start: 0.9269 (m) cc_final: 0.9050 (p) REVERT: N 251 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8763 (mm-40) REVERT: N 285 LEU cc_start: 0.9086 (mm) cc_final: 0.8737 (mt) REVERT: N 345 LYS cc_start: 0.8991 (mttp) cc_final: 0.8615 (mttm) REVERT: H 56 LEU cc_start: 0.7540 (mt) cc_final: 0.6935 (tt) REVERT: H 64 ILE cc_start: 0.9252 (mt) cc_final: 0.9010 (tp) REVERT: H 65 LYS cc_start: 0.8921 (tttm) cc_final: 0.8654 (tttp) REVERT: H 79 ARG cc_start: 0.7626 (mmt180) cc_final: 0.7012 (ttp80) REVERT: H 119 ASP cc_start: 0.7688 (m-30) cc_final: 0.7479 (m-30) REVERT: H 124 TYR cc_start: 0.8796 (t80) cc_final: 0.8365 (t80) REVERT: H 160 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8826 (tt) REVERT: H 166 LEU cc_start: 0.9101 (mt) cc_final: 0.8804 (tt) REVERT: H 186 VAL cc_start: 0.8786 (t) cc_final: 0.8195 (t) REVERT: H 225 GLU cc_start: 0.6635 (mt-10) cc_final: 0.6250 (mt-10) REVERT: H 268 THR cc_start: 0.7269 (p) cc_final: 0.7032 (m) REVERT: H 277 LEU cc_start: 0.8938 (tp) cc_final: 0.8524 (mm) REVERT: H 303 ASP cc_start: 0.8501 (m-30) cc_final: 0.8212 (t0) REVERT: H 304 GLN cc_start: 0.8810 (mt0) cc_final: 0.8456 (mt0) outliers start: 89 outliers final: 27 residues processed: 1398 average time/residue: 0.5036 time to fit residues: 1139.1007 Evaluate side-chains 862 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 821 time to evaluate : 4.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 385 optimal weight: 3.9990 chunk 346 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 233 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 358 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 415 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 87 HIS 1 174 HIS 1 245 GLN 1 315 HIS 1 343 ASN 2 8 GLN 2 81 GLN 2 120 GLN ** 2 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 208 HIS 3 225 ASN 3 372 GLN 3 468 HIS 4 33 GLN 4 58 HIS 4 78 ASN 4 93 HIS ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 169 HIS ** 4 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 58 ASN 6 153 GLN J 24 ASN L 109 ASN L 150 GLN L 325 HIS ** L 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 433 HIS M 183 HIS N 245 ASN ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS H 233 HIS H 304 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.264 37052 Z= 0.804 Angle : 2.300 51.220 50464 Z= 1.493 Chirality : 0.444 6.568 5664 Planarity : 0.007 0.102 6374 Dihedral : 7.333 162.392 5088 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.96 % Favored : 93.63 % Rotamer: Outliers : 0.19 % Allowed : 3.55 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.11), residues: 4612 helix: -0.72 (0.09), residues: 2457 sheet: -1.45 (0.30), residues: 266 loop : -2.66 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 79 HIS 0.023 0.002 HIS L 88 PHE 0.033 0.002 PHE H 252 TYR 0.031 0.002 TYR H 232 ARG 0.010 0.001 ARG 7 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1083 time to evaluate : 4.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 79 MET cc_start: 0.8332 (mmm) cc_final: 0.7804 (mmm) REVERT: 1 118 MET cc_start: 0.8587 (mtp) cc_final: 0.8268 (ttt) REVERT: 1 189 MET cc_start: 0.7607 (mtm) cc_final: 0.7123 (mtm) REVERT: 1 208 GLN cc_start: 0.8038 (mt0) cc_final: 0.6743 (pp30) REVERT: 1 338 VAL cc_start: 0.8010 (t) cc_final: 0.7741 (p) REVERT: 2 81 GLN cc_start: 0.8146 (mt0) cc_final: 0.7807 (mt0) REVERT: 2 141 TYR cc_start: 0.7070 (m-80) cc_final: 0.6816 (m-10) REVERT: 3 3 ARG cc_start: 0.7043 (mmp-170) cc_final: 0.6656 (mtp85) REVERT: 3 139 LEU cc_start: 0.7013 (tt) cc_final: 0.6483 (pp) REVERT: 3 175 ILE cc_start: 0.9392 (tt) cc_final: 0.9178 (mt) REVERT: 3 176 LEU cc_start: 0.8749 (tp) cc_final: 0.8502 (tp) REVERT: 3 236 LEU cc_start: 0.8782 (mt) cc_final: 0.8564 (mt) REVERT: 3 239 THR cc_start: 0.8658 (m) cc_final: 0.8030 (t) REVERT: 3 249 MET cc_start: 0.8681 (mmt) cc_final: 0.8296 (mmm) REVERT: 3 288 ILE cc_start: 0.8858 (pt) cc_final: 0.8554 (mt) REVERT: 3 307 LYS cc_start: 0.7449 (mttt) cc_final: 0.6864 (mttt) REVERT: 3 395 PHE cc_start: 0.8745 (t80) cc_final: 0.8327 (t80) REVERT: 3 494 LYS cc_start: 0.8478 (tttt) cc_final: 0.8207 (ttpp) REVERT: 3 547 MET cc_start: 0.8429 (tpp) cc_final: 0.8221 (tpp) REVERT: 4 93 HIS cc_start: 0.8555 (m-70) cc_final: 0.7826 (m-70) REVERT: 4 151 ARG cc_start: 0.7390 (tmm160) cc_final: 0.7163 (ttp80) REVERT: 4 208 PHE cc_start: 0.7515 (m-10) cc_final: 0.7203 (m-10) REVERT: 4 216 GLU cc_start: 0.5250 (mt-10) cc_final: 0.4703 (mt-10) REVERT: 4 230 ILE cc_start: 0.8951 (mt) cc_final: 0.8728 (mm) REVERT: 4 276 MET cc_start: 0.8898 (mmt) cc_final: 0.8498 (tpp) REVERT: 4 283 MET cc_start: 0.8182 (mtp) cc_final: 0.7816 (ttm) REVERT: 4 321 MET cc_start: 0.9312 (tpt) cc_final: 0.9103 (tmm) REVERT: 4 322 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7722 (mt-10) REVERT: 5 22 LEU cc_start: 0.8602 (mm) cc_final: 0.8215 (mt) REVERT: 5 48 PHE cc_start: 0.7247 (t80) cc_final: 0.6993 (t80) REVERT: 5 117 GLU cc_start: 0.8492 (tt0) cc_final: 0.8245 (tt0) REVERT: 5 177 LYS cc_start: 0.8977 (mttt) cc_final: 0.8459 (mttp) REVERT: 6 51 MET cc_start: 0.8886 (mtp) cc_final: 0.8022 (ttm) REVERT: 6 78 MET cc_start: 0.9141 (ttm) cc_final: 0.8785 (ttm) REVERT: 6 113 SER cc_start: 0.9282 (m) cc_final: 0.8873 (p) REVERT: 6 114 SER cc_start: 0.9149 (m) cc_final: 0.8943 (p) REVERT: 6 170 LEU cc_start: 0.9082 (mm) cc_final: 0.8870 (mm) REVERT: 9 36 ARG cc_start: 0.8753 (mtt180) cc_final: 0.8516 (mtt90) REVERT: 9 95 MET cc_start: 0.8637 (mmm) cc_final: 0.8090 (mmm) REVERT: 9 114 VAL cc_start: 0.9164 (t) cc_final: 0.8897 (p) REVERT: 9 119 PHE cc_start: 0.8793 (p90) cc_final: 0.8128 (p90) REVERT: 9 121 MET cc_start: 0.8382 (pmm) cc_final: 0.8087 (pmm) REVERT: 9 159 VAL cc_start: 0.7822 (m) cc_final: 0.7550 (m) REVERT: 7 17 LEU cc_start: 0.8762 (mt) cc_final: 0.8499 (tp) REVERT: A 11 LEU cc_start: 0.8799 (mt) cc_final: 0.8045 (tt) REVERT: A 13 TYR cc_start: 0.8195 (t80) cc_final: 0.7682 (t80) REVERT: A 57 PHE cc_start: 0.8508 (m-80) cc_final: 0.8002 (m-80) REVERT: A 66 MET cc_start: 0.8617 (tpp) cc_final: 0.8090 (tpp) REVERT: A 72 ASP cc_start: 0.8627 (t70) cc_final: 0.8417 (t70) REVERT: A 104 PHE cc_start: 0.8643 (t80) cc_final: 0.8275 (t80) REVERT: A 108 LEU cc_start: 0.8772 (mt) cc_final: 0.8542 (tt) REVERT: A 116 MET cc_start: 0.8221 (ptm) cc_final: 0.7946 (ppp) REVERT: J 33 ILE cc_start: 0.9359 (mt) cc_final: 0.9086 (mt) REVERT: J 47 ASP cc_start: 0.7960 (t0) cc_final: 0.7651 (t0) REVERT: J 55 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8409 (tp40) REVERT: J 74 LEU cc_start: 0.8305 (tp) cc_final: 0.7997 (tp) REVERT: J 103 ILE cc_start: 0.8432 (mm) cc_final: 0.8030 (mt) REVERT: J 136 LEU cc_start: 0.8628 (pt) cc_final: 0.8024 (tp) REVERT: K 70 VAL cc_start: 0.9473 (m) cc_final: 0.9142 (p) REVERT: L 31 VAL cc_start: 0.6537 (t) cc_final: 0.6330 (t) REVERT: L 87 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9152 (tt) REVERT: L 136 LEU cc_start: 0.8970 (tp) cc_final: 0.8710 (tp) REVERT: L 153 ASP cc_start: 0.8202 (m-30) cc_final: 0.7518 (t0) REVERT: L 169 PHE cc_start: 0.8239 (t80) cc_final: 0.7879 (t80) REVERT: L 187 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7227 (pp20) REVERT: L 188 LEU cc_start: 0.9354 (tp) cc_final: 0.8659 (tp) REVERT: L 219 GLN cc_start: 0.7168 (mp10) cc_final: 0.6642 (mp10) REVERT: L 223 MET cc_start: 0.6864 (ptt) cc_final: 0.6182 (ptp) REVERT: L 261 SER cc_start: 0.9071 (p) cc_final: 0.8596 (m) REVERT: L 265 ASP cc_start: 0.6677 (p0) cc_final: 0.6472 (t0) REVERT: L 293 LYS cc_start: 0.7744 (mttm) cc_final: 0.7397 (tttt) REVERT: L 319 LEU cc_start: 0.8859 (mt) cc_final: 0.8333 (mm) REVERT: L 334 LEU cc_start: 0.8267 (mt) cc_final: 0.7574 (mt) REVERT: L 412 LEU cc_start: 0.8198 (mt) cc_final: 0.7890 (tp) REVERT: M 116 LEU cc_start: 0.6105 (tp) cc_final: 0.5716 (tp) REVERT: M 135 LEU cc_start: 0.9045 (mt) cc_final: 0.8512 (tp) REVERT: M 217 PHE cc_start: 0.8890 (t80) cc_final: 0.8631 (t80) REVERT: M 244 PHE cc_start: 0.8172 (m-80) cc_final: 0.7738 (m-80) REVERT: M 386 LYS cc_start: 0.8068 (mttm) cc_final: 0.7745 (tptp) REVERT: N 35 LEU cc_start: 0.9294 (tp) cc_final: 0.9022 (tp) REVERT: N 63 THR cc_start: 0.9270 (t) cc_final: 0.9003 (t) REVERT: N 71 LEU cc_start: 0.9269 (mt) cc_final: 0.9043 (mp) REVERT: N 79 SER cc_start: 0.8447 (m) cc_final: 0.8104 (t) REVERT: N 119 TYR cc_start: 0.9262 (m-80) cc_final: 0.8999 (m-80) REVERT: N 203 SER cc_start: 0.9102 (t) cc_final: 0.8838 (p) REVERT: N 301 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7463 (tp-100) REVERT: N 345 LYS cc_start: 0.8487 (mttp) cc_final: 0.8228 (mttm) REVERT: N 410 LEU cc_start: 0.9415 (pp) cc_final: 0.9204 (tp) REVERT: N 420 LEU cc_start: 0.8687 (tp) cc_final: 0.8259 (tt) REVERT: H 56 LEU cc_start: 0.7539 (mt) cc_final: 0.7036 (tt) REVERT: H 79 ARG cc_start: 0.7758 (mmt180) cc_final: 0.7375 (ttp-170) REVERT: H 124 TYR cc_start: 0.8807 (t80) cc_final: 0.8293 (t80) REVERT: H 146 LYS cc_start: 0.8804 (mptt) cc_final: 0.8511 (mmtt) REVERT: H 235 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6833 (mp0) REVERT: H 268 THR cc_start: 0.6302 (p) cc_final: 0.6021 (m) REVERT: H 277 LEU cc_start: 0.8541 (tp) cc_final: 0.8140 (mm) REVERT: H 304 GLN cc_start: 0.8510 (mt0) cc_final: 0.8267 (mt0) outliers start: 7 outliers final: 2 residues processed: 1085 average time/residue: 0.4569 time to fit residues: 817.8683 Evaluate side-chains 787 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 784 time to evaluate : 3.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 230 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 345 optimal weight: 0.8980 chunk 282 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 415 optimal weight: 0.2980 chunk 449 optimal weight: 0.9980 chunk 370 optimal weight: 2.9990 chunk 412 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 333 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 87 HIS 1 420 GLN 2 129 HIS 2 137 ASN ** 2 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 38 HIS 3 163 HIS 3 183 HIS ** 3 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 468 HIS ** 3 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 120 ASN K 39 ASN M 411 GLN ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.266 37052 Z= 0.770 Angle : 2.256 51.057 50464 Z= 1.472 Chirality : 0.445 6.528 5664 Planarity : 0.006 0.105 6374 Dihedral : 6.634 166.126 5088 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.44 % Favored : 94.30 % Rotamer: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.12), residues: 4612 helix: 0.34 (0.10), residues: 2438 sheet: -1.31 (0.28), residues: 313 loop : -2.20 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 79 HIS 0.012 0.001 HIS 9 41 PHE 0.031 0.002 PHE N 137 TYR 0.041 0.002 TYR H 147 ARG 0.010 0.001 ARG 6 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1008 time to evaluate : 4.387 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: 1 79 MET cc_start: 0.8334 (mmm) cc_final: 0.8011 (mmm) REVERT: 1 147 GLN cc_start: 0.8054 (tp40) cc_final: 0.7703 (tp40) REVERT: 1 222 GLU cc_start: 0.8002 (tt0) cc_final: 0.7653 (tt0) REVERT: 1 376 THR cc_start: 0.8398 (p) cc_final: 0.7974 (t) REVERT: 3 3 ARG cc_start: 0.7127 (mmp-170) cc_final: 0.6728 (mtp85) REVERT: 3 21 ASP cc_start: 0.8956 (m-30) cc_final: 0.8753 (t0) REVERT: 3 139 LEU cc_start: 0.6815 (tt) cc_final: 0.6459 (pp) REVERT: 3 155 THR cc_start: 0.8095 (m) cc_final: 0.7872 (m) REVERT: 3 239 THR cc_start: 0.8729 (m) cc_final: 0.8025 (t) REVERT: 3 249 MET cc_start: 0.8674 (mmt) cc_final: 0.8316 (mmm) REVERT: 3 288 ILE cc_start: 0.8781 (pt) cc_final: 0.8542 (mt) REVERT: 3 420 LEU cc_start: 0.7890 (tp) cc_final: 0.7644 (tp) REVERT: 3 494 LYS cc_start: 0.8442 (tttt) cc_final: 0.7994 (ttpp) REVERT: 3 547 MET cc_start: 0.8447 (tpp) cc_final: 0.8194 (tpp) REVERT: 4 93 HIS cc_start: 0.8446 (m-70) cc_final: 0.7833 (m-70) REVERT: 4 130 LEU cc_start: 0.8978 (mm) cc_final: 0.8752 (mm) REVERT: 4 169 HIS cc_start: 0.7585 (m-70) cc_final: 0.7278 (m170) REVERT: 4 216 GLU cc_start: 0.5365 (mt-10) cc_final: 0.4732 (mt-10) REVERT: 4 230 ILE cc_start: 0.8967 (mt) cc_final: 0.8745 (mm) REVERT: 4 276 MET cc_start: 0.8865 (mmt) cc_final: 0.8509 (tpp) REVERT: 4 283 MET cc_start: 0.8186 (mtp) cc_final: 0.7812 (ttm) REVERT: 4 385 CYS cc_start: 0.7763 (p) cc_final: 0.7303 (p) REVERT: 5 122 PHE cc_start: 0.8910 (m-80) cc_final: 0.8557 (m-10) REVERT: 5 146 LEU cc_start: 0.9218 (mt) cc_final: 0.8992 (tt) REVERT: 5 177 LYS cc_start: 0.8846 (mttt) cc_final: 0.8397 (mttp) REVERT: 6 51 MET cc_start: 0.8809 (mtp) cc_final: 0.8036 (ttm) REVERT: 6 108 MET cc_start: 0.8840 (ttt) cc_final: 0.8636 (ttt) REVERT: 6 113 SER cc_start: 0.9389 (m) cc_final: 0.9084 (p) REVERT: 6 134 ASP cc_start: 0.9296 (m-30) cc_final: 0.8780 (m-30) REVERT: 9 12 ILE cc_start: 0.8461 (tp) cc_final: 0.8219 (tp) REVERT: 9 36 ARG cc_start: 0.8694 (mtt180) cc_final: 0.8105 (mmt90) REVERT: 9 114 VAL cc_start: 0.9007 (t) cc_final: 0.8686 (p) REVERT: 9 119 PHE cc_start: 0.8705 (p90) cc_final: 0.8234 (p90) REVERT: 9 163 VAL cc_start: 0.9278 (t) cc_final: 0.9058 (m) REVERT: 7 17 LEU cc_start: 0.8818 (mt) cc_final: 0.8490 (tp) REVERT: A 11 LEU cc_start: 0.8903 (mt) cc_final: 0.8292 (tt) REVERT: A 57 PHE cc_start: 0.8550 (m-80) cc_final: 0.8066 (m-80) REVERT: A 74 GLU cc_start: 0.8085 (tt0) cc_final: 0.7871 (tt0) REVERT: A 81 TYR cc_start: 0.8318 (t80) cc_final: 0.7688 (t80) REVERT: A 116 MET cc_start: 0.8337 (ptm) cc_final: 0.7882 (ppp) REVERT: J 47 ASP cc_start: 0.7929 (t0) cc_final: 0.7324 (t0) REVERT: J 136 LEU cc_start: 0.8520 (pt) cc_final: 0.8026 (tp) REVERT: K 70 VAL cc_start: 0.9241 (m) cc_final: 0.8915 (p) REVERT: L 153 ASP cc_start: 0.8037 (m-30) cc_final: 0.7435 (t0) REVERT: L 162 ASN cc_start: 0.8095 (m-40) cc_final: 0.7670 (t0) REVERT: L 187 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6617 (pp20) REVERT: L 189 LYS cc_start: 0.8613 (ptmt) cc_final: 0.8378 (ptpt) REVERT: L 219 GLN cc_start: 0.7266 (mp10) cc_final: 0.6583 (mp10) REVERT: L 334 LEU cc_start: 0.8224 (mt) cc_final: 0.7597 (mt) REVERT: L 373 LEU cc_start: 0.7042 (tp) cc_final: 0.6781 (tp) REVERT: L 451 LEU cc_start: 0.7323 (tp) cc_final: 0.7030 (tt) REVERT: M 18 LEU cc_start: 0.6428 (pt) cc_final: 0.6005 (mm) REVERT: M 116 LEU cc_start: 0.5853 (tp) cc_final: 0.5628 (tp) REVERT: M 135 LEU cc_start: 0.9125 (mt) cc_final: 0.8520 (tp) REVERT: M 244 PHE cc_start: 0.7989 (m-80) cc_final: 0.7546 (m-80) REVERT: M 248 LEU cc_start: 0.8964 (pp) cc_final: 0.8647 (mm) REVERT: M 251 GLU cc_start: 0.7404 (mp0) cc_final: 0.6676 (tp30) REVERT: M 386 LYS cc_start: 0.7698 (mttm) cc_final: 0.7372 (mttt) REVERT: M 457 LEU cc_start: 0.8244 (mm) cc_final: 0.7915 (mm) REVERT: N 35 LEU cc_start: 0.9301 (tp) cc_final: 0.9020 (tp) REVERT: N 63 THR cc_start: 0.9172 (t) cc_final: 0.8914 (t) REVERT: N 105 LEU cc_start: 0.8727 (mt) cc_final: 0.8511 (mt) REVERT: N 119 TYR cc_start: 0.9288 (m-80) cc_final: 0.8970 (m-80) REVERT: N 210 PHE cc_start: 0.7983 (t80) cc_final: 0.7025 (t80) REVERT: N 345 LYS cc_start: 0.8501 (mttp) cc_final: 0.8209 (mttm) REVERT: N 420 LEU cc_start: 0.8819 (tp) cc_final: 0.8471 (tt) REVERT: H 54 PHE cc_start: 0.7202 (t80) cc_final: 0.6530 (t80) REVERT: H 56 LEU cc_start: 0.7684 (mt) cc_final: 0.7151 (tt) REVERT: H 79 ARG cc_start: 0.7762 (mmt180) cc_final: 0.7334 (ttp-170) REVERT: H 84 LEU cc_start: 0.9240 (tp) cc_final: 0.8634 (tp) REVERT: H 124 TYR cc_start: 0.8648 (t80) cc_final: 0.7950 (t80) REVERT: H 148 SER cc_start: 0.7689 (m) cc_final: 0.7323 (t) REVERT: H 181 ASN cc_start: 0.7981 (m-40) cc_final: 0.7561 (t0) REVERT: H 277 LEU cc_start: 0.8283 (tp) cc_final: 0.8003 (mm) REVERT: H 283 ILE cc_start: 0.9138 (mt) cc_final: 0.8916 (tt) REVERT: H 290 PHE cc_start: 0.7056 (m-10) cc_final: 0.6415 (m-10) REVERT: H 314 PHE cc_start: 0.8207 (t80) cc_final: 0.7745 (t80) outliers start: 1 outliers final: 0 residues processed: 1008 average time/residue: 0.4635 time to fit residues: 780.2584 Evaluate side-chains 754 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 754 time to evaluate : 3.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 410 optimal weight: 0.0040 chunk 312 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 279 optimal weight: 10.0000 chunk 417 optimal weight: 4.9990 chunk 441 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 chunk 395 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 129 HIS ** 2 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 392 GLN ** 3 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 661 GLN 4 63 HIS ** 4 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 24 ASN 6 120 ASN 9 46 HIS J 55 GLN L 582 GLN H 183 ASN H 304 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.269 37052 Z= 0.780 Angle : 2.271 51.001 50464 Z= 1.478 Chirality : 0.445 6.567 5664 Planarity : 0.006 0.057 6374 Dihedral : 6.436 166.654 5088 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.64 % Favored : 94.08 % Rotamer: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.98 (0.12), residues: 4612 helix: 0.47 (0.10), residues: 2440 sheet: -1.20 (0.29), residues: 310 loop : -2.09 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 79 HIS 0.010 0.002 HIS 9 41 PHE 0.052 0.002 PHE H 30 TYR 0.028 0.002 TYR M 405 ARG 0.014 0.001 ARG H 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 895 time to evaluate : 3.994 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: 1 79 MET cc_start: 0.8365 (mmm) cc_final: 0.7924 (mmm) REVERT: 1 147 GLN cc_start: 0.7874 (tp40) cc_final: 0.7594 (tp40) REVERT: 1 268 MET cc_start: 0.7402 (mpp) cc_final: 0.6432 (mpp) REVERT: 1 317 GLN cc_start: 0.8269 (pt0) cc_final: 0.8030 (pt0) REVERT: 1 376 THR cc_start: 0.8464 (p) cc_final: 0.8215 (m) REVERT: 2 101 THR cc_start: 0.8813 (p) cc_final: 0.8541 (t) REVERT: 3 132 ASP cc_start: 0.9227 (m-30) cc_final: 0.8891 (m-30) REVERT: 3 139 LEU cc_start: 0.7123 (tt) cc_final: 0.6759 (pp) REVERT: 3 179 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8840 (mt-10) REVERT: 3 239 THR cc_start: 0.8857 (m) cc_final: 0.8526 (p) REVERT: 3 249 MET cc_start: 0.8747 (mmt) cc_final: 0.8444 (mmm) REVERT: 3 420 LEU cc_start: 0.8088 (tp) cc_final: 0.7833 (tp) REVERT: 3 426 TYR cc_start: 0.7283 (m-80) cc_final: 0.6341 (m-80) REVERT: 3 494 LYS cc_start: 0.8658 (tttt) cc_final: 0.8020 (ttpp) REVERT: 3 769 LEU cc_start: 0.7478 (mp) cc_final: 0.7176 (mp) REVERT: 4 93 HIS cc_start: 0.8463 (m-70) cc_final: 0.8077 (m-70) REVERT: 4 103 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8772 (tttt) REVERT: 4 285 GLU cc_start: 0.6825 (tt0) cc_final: 0.6458 (tp30) REVERT: 4 385 CYS cc_start: 0.8026 (p) cc_final: 0.7737 (p) REVERT: 4 393 MET cc_start: 0.8087 (tpt) cc_final: 0.7768 (tpt) REVERT: 5 115 GLU cc_start: 0.8837 (tp30) cc_final: 0.8592 (tp30) REVERT: 5 122 PHE cc_start: 0.9128 (m-80) cc_final: 0.8515 (m-10) REVERT: 5 146 LEU cc_start: 0.9307 (mt) cc_final: 0.9037 (tt) REVERT: 6 51 MET cc_start: 0.8646 (mtp) cc_final: 0.8201 (ttm) REVERT: 6 108 MET cc_start: 0.8938 (ttt) cc_final: 0.8662 (ttt) REVERT: 6 114 SER cc_start: 0.8580 (p) cc_final: 0.8343 (p) REVERT: 6 134 ASP cc_start: 0.9481 (m-30) cc_final: 0.9068 (m-30) REVERT: 9 90 VAL cc_start: 0.8922 (t) cc_final: 0.8700 (t) REVERT: 9 99 ILE cc_start: 0.9179 (tt) cc_final: 0.8912 (tt) REVERT: 9 119 PHE cc_start: 0.8788 (p90) cc_final: 0.8451 (p90) REVERT: 9 163 VAL cc_start: 0.9317 (t) cc_final: 0.9051 (m) REVERT: 7 17 LEU cc_start: 0.8897 (mt) cc_final: 0.8545 (tp) REVERT: 7 91 ILE cc_start: 0.8664 (mm) cc_final: 0.8382 (mt) REVERT: A 11 LEU cc_start: 0.8963 (mt) cc_final: 0.8321 (tt) REVERT: A 57 PHE cc_start: 0.8581 (m-80) cc_final: 0.8138 (m-80) REVERT: A 79 TRP cc_start: 0.8373 (m-90) cc_final: 0.8148 (m-90) REVERT: A 81 TYR cc_start: 0.8496 (t80) cc_final: 0.7876 (t80) REVERT: J 47 ASP cc_start: 0.8705 (t0) cc_final: 0.7851 (t0) REVERT: J 119 LEU cc_start: 0.9190 (mp) cc_final: 0.8653 (mp) REVERT: J 136 LEU cc_start: 0.8543 (pt) cc_final: 0.8085 (tp) REVERT: J 142 VAL cc_start: 0.9165 (t) cc_final: 0.8920 (t) REVERT: K 34 MET cc_start: 0.8222 (mtp) cc_final: 0.7965 (mtp) REVERT: K 70 VAL cc_start: 0.9278 (m) cc_final: 0.8971 (p) REVERT: K 89 ASP cc_start: 0.7813 (t0) cc_final: 0.7485 (t70) REVERT: L 153 ASP cc_start: 0.8169 (m-30) cc_final: 0.7814 (t0) REVERT: L 169 PHE cc_start: 0.8370 (t80) cc_final: 0.7985 (t80) REVERT: L 187 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6588 (pp20) REVERT: L 219 GLN cc_start: 0.7833 (mp10) cc_final: 0.7626 (mp10) REVERT: L 244 THR cc_start: 0.6786 (p) cc_final: 0.6532 (p) REVERT: L 290 ASP cc_start: 0.7941 (m-30) cc_final: 0.7631 (m-30) REVERT: L 334 LEU cc_start: 0.7946 (mt) cc_final: 0.7573 (mt) REVERT: M 67 LEU cc_start: 0.9149 (tp) cc_final: 0.8878 (tp) REVERT: M 122 PHE cc_start: 0.8874 (t80) cc_final: 0.8670 (t80) REVERT: M 135 LEU cc_start: 0.9158 (mt) cc_final: 0.8449 (tp) REVERT: M 244 PHE cc_start: 0.8138 (m-80) cc_final: 0.7697 (m-80) REVERT: M 251 GLU cc_start: 0.7612 (mp0) cc_final: 0.6745 (tp30) REVERT: M 435 LEU cc_start: 0.9266 (tp) cc_final: 0.9055 (tp) REVERT: M 457 LEU cc_start: 0.8351 (mm) cc_final: 0.8097 (mm) REVERT: N 35 LEU cc_start: 0.9298 (tp) cc_final: 0.9035 (tp) REVERT: N 261 SER cc_start: 0.9323 (m) cc_final: 0.8858 (p) REVERT: N 345 LYS cc_start: 0.8852 (mttp) cc_final: 0.8397 (mttm) REVERT: N 420 LEU cc_start: 0.8866 (tp) cc_final: 0.8513 (tt) REVERT: H 79 ARG cc_start: 0.7688 (mmt180) cc_final: 0.7218 (ttp80) REVERT: H 124 TYR cc_start: 0.8623 (t80) cc_final: 0.8072 (t80) REVERT: H 148 SER cc_start: 0.7848 (m) cc_final: 0.7552 (t) REVERT: H 170 LEU cc_start: 0.9207 (mt) cc_final: 0.8983 (tp) REVERT: H 211 MET cc_start: 0.8437 (mmt) cc_final: 0.8232 (mmt) REVERT: H 273 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6679 (mm-30) REVERT: H 277 LEU cc_start: 0.8399 (tp) cc_final: 0.8046 (mm) REVERT: H 283 ILE cc_start: 0.8964 (mt) cc_final: 0.8484 (tt) REVERT: H 304 GLN cc_start: 0.8481 (mt0) cc_final: 0.8229 (mt0) REVERT: H 314 PHE cc_start: 0.8339 (t80) cc_final: 0.7991 (t80) REVERT: H 328 VAL cc_start: 0.8406 (t) cc_final: 0.8129 (t) outliers start: 2 outliers final: 1 residues processed: 896 average time/residue: 0.4522 time to fit residues: 679.4016 Evaluate side-chains 675 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 674 time to evaluate : 3.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 367 optimal weight: 10.0000 chunk 250 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 328 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 chunk 376 optimal weight: 6.9990 chunk 305 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 225 optimal weight: 10.0000 chunk 396 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 420 GLN 2 129 HIS ** 2 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 347 HIS 3 465 HIS ** 3 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 129 HIS 4 330 HIS ** L 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 582 GLN ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.264 37052 Z= 0.769 Angle : 2.256 50.886 50464 Z= 1.472 Chirality : 0.444 6.465 5664 Planarity : 0.005 0.075 6374 Dihedral : 6.289 166.771 5088 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.40 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.12), residues: 4612 helix: 0.57 (0.10), residues: 2423 sheet: -1.07 (0.30), residues: 300 loop : -1.97 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 79 HIS 0.016 0.001 HIS 2 174 PHE 0.031 0.002 PHE M 201 TYR 0.022 0.002 TYR H 147 ARG 0.009 0.000 ARG 6 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 885 time to evaluate : 3.948 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: 1 79 MET cc_start: 0.8337 (mmm) cc_final: 0.7901 (mmm) REVERT: 1 147 GLN cc_start: 0.7665 (tp40) cc_final: 0.7416 (tp40) REVERT: 1 268 MET cc_start: 0.7482 (mpp) cc_final: 0.6616 (mpp) REVERT: 1 376 THR cc_start: 0.8479 (p) cc_final: 0.8267 (m) REVERT: 2 78 TYR cc_start: 0.7978 (m-10) cc_final: 0.7615 (m-10) REVERT: 2 89 LYS cc_start: 0.8578 (tptp) cc_final: 0.8314 (tptp) REVERT: 3 132 ASP cc_start: 0.9220 (m-30) cc_final: 0.8797 (m-30) REVERT: 3 237 ASP cc_start: 0.8629 (t0) cc_final: 0.8377 (t0) REVERT: 3 239 THR cc_start: 0.8824 (m) cc_final: 0.7826 (p) REVERT: 3 249 MET cc_start: 0.8885 (mmt) cc_final: 0.8611 (mmm) REVERT: 4 93 HIS cc_start: 0.8451 (m-70) cc_final: 0.7837 (m-70) REVERT: 4 130 LEU cc_start: 0.9377 (mm) cc_final: 0.9118 (mm) REVERT: 4 140 LEU cc_start: 0.7758 (tp) cc_final: 0.7540 (tp) REVERT: 4 285 GLU cc_start: 0.6709 (tt0) cc_final: 0.6403 (tp30) REVERT: 4 393 MET cc_start: 0.7894 (tpt) cc_final: 0.7011 (tpt) REVERT: 5 115 GLU cc_start: 0.8857 (tp30) cc_final: 0.8566 (tp30) REVERT: 5 122 PHE cc_start: 0.9144 (m-80) cc_final: 0.8402 (m-10) REVERT: 5 146 LEU cc_start: 0.9370 (mt) cc_final: 0.9071 (tt) REVERT: 6 51 MET cc_start: 0.8657 (mtp) cc_final: 0.8175 (ttm) REVERT: 6 108 MET cc_start: 0.8927 (ttt) cc_final: 0.8693 (ttt) REVERT: 6 114 SER cc_start: 0.8556 (p) cc_final: 0.8320 (p) REVERT: 6 134 ASP cc_start: 0.9502 (m-30) cc_final: 0.8999 (m-30) REVERT: 9 12 ILE cc_start: 0.8562 (tp) cc_final: 0.8229 (tp) REVERT: 9 119 PHE cc_start: 0.8778 (p90) cc_final: 0.8417 (p90) REVERT: 7 17 LEU cc_start: 0.8737 (mt) cc_final: 0.8536 (tp) REVERT: 7 91 ILE cc_start: 0.8734 (mm) cc_final: 0.8393 (mt) REVERT: 7 108 ILE cc_start: 0.8353 (mp) cc_final: 0.7939 (mp) REVERT: A 11 LEU cc_start: 0.8777 (mt) cc_final: 0.8106 (tt) REVERT: A 57 PHE cc_start: 0.8595 (m-80) cc_final: 0.8189 (m-80) REVERT: A 66 MET cc_start: 0.9101 (tpp) cc_final: 0.8800 (tpt) REVERT: A 72 ASP cc_start: 0.8500 (t70) cc_final: 0.8265 (t70) REVERT: A 74 GLU cc_start: 0.8124 (tt0) cc_final: 0.7850 (tt0) REVERT: A 81 TYR cc_start: 0.8507 (t80) cc_final: 0.8041 (t80) REVERT: J 47 ASP cc_start: 0.8789 (t0) cc_final: 0.7861 (t0) REVERT: J 119 LEU cc_start: 0.9158 (mp) cc_final: 0.8854 (mp) REVERT: J 136 LEU cc_start: 0.8499 (pt) cc_final: 0.8114 (tp) REVERT: K 70 VAL cc_start: 0.9218 (m) cc_final: 0.8834 (p) REVERT: K 89 ASP cc_start: 0.7904 (t0) cc_final: 0.7586 (t70) REVERT: L 153 ASP cc_start: 0.8085 (m-30) cc_final: 0.7758 (t0) REVERT: L 169 PHE cc_start: 0.8425 (t80) cc_final: 0.8073 (t80) REVERT: L 187 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6529 (pp20) REVERT: L 334 LEU cc_start: 0.8063 (mt) cc_final: 0.7655 (mt) REVERT: L 578 LEU cc_start: 0.9297 (mt) cc_final: 0.9090 (mt) REVERT: M 67 LEU cc_start: 0.9157 (tp) cc_final: 0.8921 (tp) REVERT: M 122 PHE cc_start: 0.8926 (t80) cc_final: 0.8580 (t80) REVERT: M 131 LEU cc_start: 0.9022 (mt) cc_final: 0.8818 (mt) REVERT: M 135 LEU cc_start: 0.9184 (mt) cc_final: 0.8443 (tp) REVERT: M 204 LYS cc_start: 0.8485 (tppt) cc_final: 0.8097 (tppp) REVERT: M 232 THR cc_start: 0.8195 (m) cc_final: 0.7897 (p) REVERT: M 244 PHE cc_start: 0.8210 (m-80) cc_final: 0.7759 (m-80) REVERT: M 251 GLU cc_start: 0.7599 (mp0) cc_final: 0.6638 (tp30) REVERT: M 434 LEU cc_start: 0.9014 (mm) cc_final: 0.8684 (pp) REVERT: N 35 LEU cc_start: 0.9229 (tp) cc_final: 0.8944 (tp) REVERT: N 261 SER cc_start: 0.9257 (m) cc_final: 0.8811 (p) REVERT: N 345 LYS cc_start: 0.8887 (mttp) cc_final: 0.8402 (mttm) REVERT: N 420 LEU cc_start: 0.8781 (tp) cc_final: 0.8480 (tt) REVERT: H 31 MET cc_start: 0.6963 (tmm) cc_final: 0.6741 (ttp) REVERT: H 79 ARG cc_start: 0.7556 (mmt180) cc_final: 0.7185 (ttp-170) REVERT: H 124 TYR cc_start: 0.8493 (t80) cc_final: 0.8094 (t80) REVERT: H 148 SER cc_start: 0.7850 (m) cc_final: 0.7481 (t) REVERT: H 186 VAL cc_start: 0.8774 (t) cc_final: 0.8379 (t) REVERT: H 189 GLN cc_start: 0.8287 (mp10) cc_final: 0.7676 (mp10) REVERT: H 253 ILE cc_start: 0.9400 (pt) cc_final: 0.9189 (pt) REVERT: H 277 LEU cc_start: 0.8315 (tp) cc_final: 0.7947 (mm) REVERT: H 314 PHE cc_start: 0.8391 (t80) cc_final: 0.8102 (t80) REVERT: H 328 VAL cc_start: 0.8585 (t) cc_final: 0.8309 (t) outliers start: 0 outliers final: 0 residues processed: 885 average time/residue: 0.4433 time to fit residues: 660.2601 Evaluate side-chains 687 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 4.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 148 optimal weight: 3.9990 chunk 397 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 442 optimal weight: 0.7980 chunk 367 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 146 optimal weight: 0.6980 chunk 232 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 369 ASN 1 420 GLN 2 129 HIS ** 2 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 286 ASN ** 3 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 389 GLN J 55 GLN L 467 ASN L 539 ASN L 582 GLN ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.266 37052 Z= 0.770 Angle : 2.256 51.145 50464 Z= 1.471 Chirality : 0.444 6.479 5664 Planarity : 0.005 0.064 6374 Dihedral : 6.225 167.688 5088 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.55 % Favored : 94.19 % Rotamer: Outliers : 0.05 % Allowed : 2.65 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.12), residues: 4612 helix: 0.58 (0.10), residues: 2425 sheet: -0.99 (0.30), residues: 299 loop : -1.95 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 79 HIS 0.024 0.002 HIS 2 177 PHE 0.030 0.002 PHE 4 160 TYR 0.030 0.002 TYR M 405 ARG 0.012 0.001 ARG 6 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 859 time to evaluate : 4.106 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: 1 79 MET cc_start: 0.8367 (mmm) cc_final: 0.7928 (mmm) REVERT: 1 268 MET cc_start: 0.7874 (mpp) cc_final: 0.7144 (mpp) REVERT: 1 376 THR cc_start: 0.8518 (p) cc_final: 0.8277 (m) REVERT: 2 78 TYR cc_start: 0.8010 (m-10) cc_final: 0.7602 (m-10) REVERT: 2 89 LYS cc_start: 0.8604 (tptp) cc_final: 0.8203 (tptp) REVERT: 3 132 ASP cc_start: 0.9203 (m-30) cc_final: 0.8782 (m-30) REVERT: 3 200 LEU cc_start: 0.9044 (mm) cc_final: 0.8744 (mm) REVERT: 3 237 ASP cc_start: 0.8703 (t0) cc_final: 0.8409 (t0) REVERT: 3 239 THR cc_start: 0.8079 (m) cc_final: 0.7836 (p) REVERT: 3 415 GLU cc_start: 0.8300 (pm20) cc_final: 0.7807 (mp0) REVERT: 3 558 TRP cc_start: 0.6353 (p-90) cc_final: 0.5946 (p-90) REVERT: 4 130 LEU cc_start: 0.9324 (mm) cc_final: 0.8925 (mm) REVERT: 5 146 LEU cc_start: 0.9383 (mt) cc_final: 0.9114 (tt) REVERT: 6 108 MET cc_start: 0.8901 (ttt) cc_final: 0.8643 (ttt) REVERT: 6 114 SER cc_start: 0.8575 (p) cc_final: 0.8298 (p) REVERT: 9 12 ILE cc_start: 0.8665 (tp) cc_final: 0.8346 (tp) REVERT: 9 95 MET cc_start: 0.8748 (mmm) cc_final: 0.8045 (mmm) REVERT: 9 119 PHE cc_start: 0.8846 (p90) cc_final: 0.8480 (p90) REVERT: 9 135 ASP cc_start: 0.8362 (m-30) cc_final: 0.7569 (t0) REVERT: 7 17 LEU cc_start: 0.8823 (mt) cc_final: 0.8516 (tp) REVERT: 7 91 ILE cc_start: 0.8456 (mm) cc_final: 0.8186 (mt) REVERT: A 11 LEU cc_start: 0.8590 (mt) cc_final: 0.8116 (tt) REVERT: A 57 PHE cc_start: 0.8540 (m-80) cc_final: 0.8219 (m-80) REVERT: A 81 TYR cc_start: 0.8550 (t80) cc_final: 0.8019 (t80) REVERT: J 47 ASP cc_start: 0.8848 (t0) cc_final: 0.7880 (t0) REVERT: J 119 LEU cc_start: 0.9204 (mp) cc_final: 0.8890 (mp) REVERT: J 136 LEU cc_start: 0.8429 (pt) cc_final: 0.8138 (tp) REVERT: K 61 ILE cc_start: 0.9422 (mm) cc_final: 0.8953 (mm) REVERT: K 70 VAL cc_start: 0.9160 (m) cc_final: 0.8766 (p) REVERT: L 169 PHE cc_start: 0.8415 (t80) cc_final: 0.7899 (t80) REVERT: L 173 MET cc_start: 0.8673 (mmm) cc_final: 0.8176 (tpp) REVERT: L 334 LEU cc_start: 0.7958 (mt) cc_final: 0.7555 (mt) REVERT: M 67 LEU cc_start: 0.9110 (tp) cc_final: 0.8897 (tp) REVERT: M 122 PHE cc_start: 0.8967 (t80) cc_final: 0.8624 (t80) REVERT: M 132 MET cc_start: 0.8995 (ptm) cc_final: 0.8722 (ptp) REVERT: M 135 LEU cc_start: 0.9170 (mt) cc_final: 0.8390 (tp) REVERT: M 204 LYS cc_start: 0.8505 (tppt) cc_final: 0.8111 (tppp) REVERT: M 244 PHE cc_start: 0.8339 (m-80) cc_final: 0.7994 (m-80) REVERT: M 251 GLU cc_start: 0.7522 (mp0) cc_final: 0.6559 (tp30) REVERT: M 434 LEU cc_start: 0.9231 (mm) cc_final: 0.8922 (pp) REVERT: N 35 LEU cc_start: 0.9258 (tp) cc_final: 0.8955 (tp) REVERT: N 135 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8677 (mttp) REVERT: N 261 SER cc_start: 0.9242 (m) cc_final: 0.8804 (p) REVERT: N 345 LYS cc_start: 0.9019 (mttp) cc_final: 0.8521 (mttm) REVERT: N 420 LEU cc_start: 0.8748 (tp) cc_final: 0.8410 (tt) REVERT: H 16 LYS cc_start: 0.5631 (tttp) cc_final: 0.5362 (tttp) REVERT: H 33 LEU cc_start: 0.9545 (mm) cc_final: 0.8855 (tt) REVERT: H 79 ARG cc_start: 0.7689 (mmt180) cc_final: 0.6890 (ttp-170) REVERT: H 181 ASN cc_start: 0.8119 (m-40) cc_final: 0.7835 (t0) REVERT: H 183 ASN cc_start: 0.8847 (m-40) cc_final: 0.8575 (t0) REVERT: H 186 VAL cc_start: 0.8874 (t) cc_final: 0.8474 (t) REVERT: H 189 GLN cc_start: 0.8459 (mp10) cc_final: 0.7915 (mp10) REVERT: H 277 LEU cc_start: 0.8397 (tp) cc_final: 0.8053 (mm) REVERT: H 314 PHE cc_start: 0.8569 (t80) cc_final: 0.8270 (t80) REVERT: H 328 VAL cc_start: 0.8582 (t) cc_final: 0.8294 (t) outliers start: 2 outliers final: 2 residues processed: 860 average time/residue: 0.4698 time to fit residues: 681.6099 Evaluate side-chains 658 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 656 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 426 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 251 optimal weight: 5.9990 chunk 322 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 372 optimal weight: 10.0000 chunk 246 optimal weight: 0.7980 chunk 440 optimal weight: 3.9990 chunk 275 optimal weight: 7.9990 chunk 268 optimal weight: 3.9990 chunk 203 optimal weight: 0.0170 overall best weight: 1.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 369 ASN 1 420 GLN 2 129 HIS ** 2 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 225 ASN ** 3 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 389 GLN ** 5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 HIS ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.255 37052 Z= 0.762 Angle : 2.246 50.868 50464 Z= 1.468 Chirality : 0.444 6.503 5664 Planarity : 0.005 0.069 6374 Dihedral : 6.091 168.452 5088 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.12 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.12), residues: 4612 helix: 0.64 (0.11), residues: 2420 sheet: -0.97 (0.30), residues: 289 loop : -1.82 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP L 316 HIS 0.021 0.001 HIS 2 177 PHE 0.028 0.002 PHE N 137 TYR 0.019 0.001 TYR L 416 ARG 0.006 0.000 ARG M 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 862 time to evaluate : 4.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 79 MET cc_start: 0.8336 (mmm) cc_final: 0.7980 (mmm) REVERT: 1 268 MET cc_start: 0.7214 (mpp) cc_final: 0.6461 (mpp) REVERT: 1 342 TRP cc_start: 0.8514 (t-100) cc_final: 0.7631 (t60) REVERT: 1 376 THR cc_start: 0.8498 (p) cc_final: 0.8235 (m) REVERT: 2 28 MET cc_start: 0.7738 (mmm) cc_final: 0.6936 (tpt) REVERT: 2 78 TYR cc_start: 0.8005 (m-10) cc_final: 0.7508 (m-10) REVERT: 2 89 LYS cc_start: 0.8645 (tptp) cc_final: 0.8046 (tptp) REVERT: 3 98 ASP cc_start: 0.8273 (p0) cc_final: 0.8050 (p0) REVERT: 3 132 ASP cc_start: 0.9245 (m-30) cc_final: 0.8787 (m-30) REVERT: 3 139 LEU cc_start: 0.7020 (tt) cc_final: 0.6749 (pp) REVERT: 3 200 LEU cc_start: 0.8849 (mm) cc_final: 0.8563 (mm) REVERT: 3 237 ASP cc_start: 0.8712 (t0) cc_final: 0.8450 (t0) REVERT: 3 239 THR cc_start: 0.8050 (m) cc_final: 0.7808 (p) REVERT: 3 395 PHE cc_start: 0.8470 (t80) cc_final: 0.8152 (t80) REVERT: 3 426 TYR cc_start: 0.6756 (m-80) cc_final: 0.6132 (m-80) REVERT: 3 558 TRP cc_start: 0.6517 (p-90) cc_final: 0.6260 (p-90) REVERT: 4 93 HIS cc_start: 0.8457 (m-70) cc_final: 0.7916 (m-70) REVERT: 4 130 LEU cc_start: 0.9382 (mm) cc_final: 0.8983 (mm) REVERT: 4 230 ILE cc_start: 0.8998 (mt) cc_final: 0.8788 (mm) REVERT: 4 385 CYS cc_start: 0.8488 (t) cc_final: 0.8085 (t) REVERT: 5 116 ARG cc_start: 0.8176 (mtp180) cc_final: 0.7721 (mtp85) REVERT: 5 122 PHE cc_start: 0.9147 (m-80) cc_final: 0.8859 (m-10) REVERT: 6 108 MET cc_start: 0.8975 (ttt) cc_final: 0.8760 (ttt) REVERT: 6 114 SER cc_start: 0.8641 (p) cc_final: 0.8382 (p) REVERT: 9 12 ILE cc_start: 0.8741 (tp) cc_final: 0.8405 (tp) REVERT: 9 93 ILE cc_start: 0.9512 (mt) cc_final: 0.9272 (mt) REVERT: 9 95 MET cc_start: 0.8716 (mmm) cc_final: 0.7992 (mmm) REVERT: 9 99 ILE cc_start: 0.8907 (tt) cc_final: 0.8682 (tt) REVERT: 9 119 PHE cc_start: 0.8793 (p90) cc_final: 0.8386 (p90) REVERT: 7 17 LEU cc_start: 0.8772 (mt) cc_final: 0.8490 (tp) REVERT: 7 91 ILE cc_start: 0.8442 (mm) cc_final: 0.8212 (mt) REVERT: 7 121 ARG cc_start: 0.8179 (mpp80) cc_final: 0.7920 (mpp80) REVERT: A 11 LEU cc_start: 0.8562 (mt) cc_final: 0.8074 (tt) REVERT: A 57 PHE cc_start: 0.8495 (m-80) cc_final: 0.8189 (m-80) REVERT: A 79 TRP cc_start: 0.8465 (m-90) cc_final: 0.7975 (m-90) REVERT: A 81 TYR cc_start: 0.8530 (t80) cc_final: 0.8046 (t80) REVERT: J 1 MET cc_start: 0.6021 (tpt) cc_final: 0.5681 (tpt) REVERT: J 47 ASP cc_start: 0.8832 (t0) cc_final: 0.7857 (t0) REVERT: J 119 LEU cc_start: 0.9169 (mp) cc_final: 0.8865 (mp) REVERT: J 136 LEU cc_start: 0.8368 (pt) cc_final: 0.8119 (tp) REVERT: J 139 LEU cc_start: 0.9472 (tt) cc_final: 0.9264 (tp) REVERT: K 39 ASN cc_start: 0.8514 (t0) cc_final: 0.8224 (t0) REVERT: K 70 VAL cc_start: 0.9058 (m) cc_final: 0.8723 (p) REVERT: L 92 ILE cc_start: 0.6800 (mt) cc_final: 0.6503 (tt) REVERT: L 169 PHE cc_start: 0.8428 (t80) cc_final: 0.8129 (t80) REVERT: L 308 LEU cc_start: 0.8215 (tp) cc_final: 0.8000 (tp) REVERT: M 122 PHE cc_start: 0.8905 (t80) cc_final: 0.8601 (t80) REVERT: M 132 MET cc_start: 0.8965 (ptm) cc_final: 0.8626 (ptp) REVERT: M 135 LEU cc_start: 0.9151 (mt) cc_final: 0.8325 (tp) REVERT: M 204 LYS cc_start: 0.8592 (tppt) cc_final: 0.8190 (tppp) REVERT: M 232 THR cc_start: 0.8116 (m) cc_final: 0.7859 (p) REVERT: M 244 PHE cc_start: 0.8361 (m-80) cc_final: 0.7996 (m-80) REVERT: M 251 GLU cc_start: 0.7420 (mp0) cc_final: 0.6450 (tp30) REVERT: N 35 LEU cc_start: 0.9177 (tp) cc_final: 0.8846 (tp) REVERT: N 251 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8784 (mm-40) REVERT: N 261 SER cc_start: 0.9198 (m) cc_final: 0.8759 (p) REVERT: N 345 LYS cc_start: 0.9019 (mttp) cc_final: 0.8546 (mttm) REVERT: N 420 LEU cc_start: 0.8641 (tp) cc_final: 0.8305 (tt) REVERT: H 79 ARG cc_start: 0.7752 (mmt180) cc_final: 0.6836 (ttp-170) REVERT: H 82 PHE cc_start: 0.8503 (t80) cc_final: 0.8290 (t80) REVERT: H 181 ASN cc_start: 0.8278 (m-40) cc_final: 0.7916 (t0) REVERT: H 183 ASN cc_start: 0.8822 (m-40) cc_final: 0.8599 (t0) REVERT: H 186 VAL cc_start: 0.8848 (t) cc_final: 0.8468 (t) REVERT: H 189 GLN cc_start: 0.8457 (mp10) cc_final: 0.7782 (mp10) REVERT: H 277 LEU cc_start: 0.8268 (tp) cc_final: 0.7984 (mm) REVERT: H 314 PHE cc_start: 0.8587 (t80) cc_final: 0.8265 (t80) REVERT: H 328 VAL cc_start: 0.8572 (t) cc_final: 0.8310 (t) outliers start: 0 outliers final: 0 residues processed: 862 average time/residue: 0.4541 time to fit residues: 658.0166 Evaluate side-chains 667 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 667 time to evaluate : 4.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 272 optimal weight: 3.9990 chunk 175 optimal weight: 9.9990 chunk 263 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 280 optimal weight: 0.9990 chunk 300 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 41 optimal weight: 0.0870 chunk 346 optimal weight: 0.9980 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 420 GLN 2 129 HIS ** 2 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 225 ASN ** 3 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 733 GLN ** 4 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 389 GLN ** 5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 582 GLN ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.261 37052 Z= 0.763 Angle : 2.246 50.815 50464 Z= 1.467 Chirality : 0.444 6.475 5664 Planarity : 0.005 0.074 6374 Dihedral : 6.018 168.739 5088 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.99 % Favored : 94.75 % Rotamer: Outliers : 0.03 % Allowed : 1.04 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.12), residues: 4612 helix: 0.65 (0.11), residues: 2426 sheet: -0.98 (0.31), residues: 289 loop : -1.72 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP L 316 HIS 0.018 0.001 HIS 2 177 PHE 0.029 0.002 PHE 3 395 TYR 0.030 0.001 TYR M 405 ARG 0.023 0.000 ARG L 529 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 860 time to evaluate : 4.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 79 MET cc_start: 0.8359 (mmm) cc_final: 0.7972 (mmm) REVERT: 1 97 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7653 (pt0) REVERT: 1 222 GLU cc_start: 0.8083 (tt0) cc_final: 0.7670 (tt0) REVERT: 1 268 MET cc_start: 0.7383 (mpp) cc_final: 0.6557 (mpp) REVERT: 1 342 TRP cc_start: 0.8590 (t-100) cc_final: 0.7499 (t60) REVERT: 1 376 THR cc_start: 0.8504 (p) cc_final: 0.7968 (t) REVERT: 1 408 TRP cc_start: 0.8164 (m-10) cc_final: 0.7901 (m-10) REVERT: 2 28 MET cc_start: 0.7553 (mmm) cc_final: 0.6820 (tpt) REVERT: 2 58 THR cc_start: 0.9059 (m) cc_final: 0.8617 (m) REVERT: 2 78 TYR cc_start: 0.7999 (m-10) cc_final: 0.7464 (m-10) REVERT: 2 89 LYS cc_start: 0.8611 (tptp) cc_final: 0.8007 (tptp) REVERT: 3 132 ASP cc_start: 0.9238 (m-30) cc_final: 0.8780 (m-30) REVERT: 3 200 LEU cc_start: 0.8883 (mm) cc_final: 0.8613 (mm) REVERT: 3 237 ASP cc_start: 0.8745 (t0) cc_final: 0.8455 (t0) REVERT: 3 239 THR cc_start: 0.8085 (m) cc_final: 0.7803 (p) REVERT: 3 426 TYR cc_start: 0.7036 (m-80) cc_final: 0.6338 (m-80) REVERT: 3 558 TRP cc_start: 0.6516 (p-90) cc_final: 0.6220 (p-90) REVERT: 4 130 LEU cc_start: 0.9239 (mm) cc_final: 0.8801 (mm) REVERT: 4 230 ILE cc_start: 0.9039 (mt) cc_final: 0.8791 (mm) REVERT: 4 385 CYS cc_start: 0.8364 (t) cc_final: 0.8119 (t) REVERT: 5 146 LEU cc_start: 0.9276 (mt) cc_final: 0.8775 (tt) REVERT: 5 185 LYS cc_start: 0.8634 (pttt) cc_final: 0.8265 (pttt) REVERT: 6 108 MET cc_start: 0.8928 (ttt) cc_final: 0.8724 (ttt) REVERT: 6 114 SER cc_start: 0.8647 (p) cc_final: 0.8346 (p) REVERT: 9 12 ILE cc_start: 0.8710 (tp) cc_final: 0.8387 (tp) REVERT: 9 95 MET cc_start: 0.8830 (mmm) cc_final: 0.8003 (mmm) REVERT: 9 99 ILE cc_start: 0.8904 (tt) cc_final: 0.8703 (tt) REVERT: 9 119 PHE cc_start: 0.8790 (p90) cc_final: 0.8396 (p90) REVERT: 7 91 ILE cc_start: 0.8430 (mm) cc_final: 0.8193 (mt) REVERT: 7 120 ASP cc_start: 0.7022 (t0) cc_final: 0.6226 (t0) REVERT: 7 121 ARG cc_start: 0.8150 (mpp80) cc_final: 0.7419 (mpp80) REVERT: A 11 LEU cc_start: 0.8743 (mt) cc_final: 0.8071 (tt) REVERT: A 57 PHE cc_start: 0.8482 (m-80) cc_final: 0.8126 (m-80) REVERT: A 79 TRP cc_start: 0.8426 (m-90) cc_final: 0.7874 (m-90) REVERT: A 81 TYR cc_start: 0.8522 (t80) cc_final: 0.8013 (t80) REVERT: J 5 GLU cc_start: 0.8045 (pt0) cc_final: 0.7702 (pp20) REVERT: J 47 ASP cc_start: 0.8770 (t0) cc_final: 0.7814 (t0) REVERT: J 72 MET cc_start: 0.7626 (mtt) cc_final: 0.7406 (mtm) REVERT: J 83 PHE cc_start: 0.4517 (m-80) cc_final: 0.3289 (p90) REVERT: J 136 LEU cc_start: 0.8415 (pt) cc_final: 0.8101 (tp) REVERT: K 15 VAL cc_start: 0.9550 (t) cc_final: 0.9327 (p) REVERT: K 39 ASN cc_start: 0.8567 (t0) cc_final: 0.8223 (t0) REVERT: K 70 VAL cc_start: 0.9038 (m) cc_final: 0.8643 (p) REVERT: L 92 ILE cc_start: 0.6777 (mt) cc_final: 0.6468 (tt) REVERT: L 169 PHE cc_start: 0.8362 (t80) cc_final: 0.8093 (t80) REVERT: M 122 PHE cc_start: 0.8890 (t80) cc_final: 0.8666 (t80) REVERT: M 132 MET cc_start: 0.8964 (ptm) cc_final: 0.8639 (ptp) REVERT: M 135 LEU cc_start: 0.9175 (mt) cc_final: 0.8363 (tp) REVERT: M 204 LYS cc_start: 0.8525 (tppt) cc_final: 0.8110 (tppp) REVERT: M 244 PHE cc_start: 0.8243 (m-80) cc_final: 0.7774 (m-10) REVERT: M 357 LEU cc_start: 0.8976 (tp) cc_final: 0.8717 (tp) REVERT: N 35 LEU cc_start: 0.9177 (tp) cc_final: 0.8845 (tp) REVERT: N 125 ARG cc_start: 0.5393 (mtm-85) cc_final: 0.5189 (mtm-85) REVERT: N 135 LYS cc_start: 0.8939 (mtmm) cc_final: 0.8684 (mttp) REVERT: N 251 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8800 (mm-40) REVERT: N 261 SER cc_start: 0.9188 (m) cc_final: 0.8694 (p) REVERT: N 345 LYS cc_start: 0.9053 (mttp) cc_final: 0.8497 (mttm) REVERT: N 420 LEU cc_start: 0.8696 (tp) cc_final: 0.8381 (tt) REVERT: H 16 LYS cc_start: 0.5914 (tttp) cc_final: 0.5670 (tttp) REVERT: H 33 LEU cc_start: 0.9513 (mm) cc_final: 0.8871 (tt) REVERT: H 35 GLU cc_start: 0.9132 (tt0) cc_final: 0.8818 (tt0) REVERT: H 79 ARG cc_start: 0.7742 (mmt180) cc_final: 0.6825 (ttp-170) REVERT: H 82 PHE cc_start: 0.8470 (t80) cc_final: 0.8243 (t80) REVERT: H 137 PHE cc_start: 0.8280 (p90) cc_final: 0.8031 (p90) REVERT: H 181 ASN cc_start: 0.8241 (m-40) cc_final: 0.7919 (t0) REVERT: H 189 GLN cc_start: 0.8414 (mp10) cc_final: 0.7901 (mp10) REVERT: H 246 MET cc_start: 0.8559 (ttp) cc_final: 0.8325 (ttp) REVERT: H 277 LEU cc_start: 0.8301 (tp) cc_final: 0.8066 (mm) REVERT: H 328 VAL cc_start: 0.8584 (t) cc_final: 0.8316 (t) outliers start: 1 outliers final: 1 residues processed: 860 average time/residue: 0.4419 time to fit residues: 639.5465 Evaluate side-chains 673 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 672 time to evaluate : 4.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 400 optimal weight: 2.9990 chunk 421 optimal weight: 7.9990 chunk 385 optimal weight: 7.9990 chunk 410 optimal weight: 0.6980 chunk 247 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 322 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 370 optimal weight: 4.9990 chunk 388 optimal weight: 1.9990 chunk 409 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 129 HIS ** 2 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 225 ASN 3 286 ASN 3 410 HIS ** 3 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 657 HIS ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 389 GLN ** 5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 ASN ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.258 37052 Z= 0.772 Angle : 2.260 50.843 50464 Z= 1.473 Chirality : 0.444 6.462 5664 Planarity : 0.005 0.082 6374 Dihedral : 6.075 168.606 5088 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.44 % Favored : 94.32 % Rotamer: Outliers : 0.03 % Allowed : 0.71 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.12), residues: 4612 helix: 0.59 (0.11), residues: 2425 sheet: -1.09 (0.31), residues: 281 loop : -1.72 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 316 HIS 0.017 0.001 HIS 2 177 PHE 0.027 0.002 PHE 4 208 TYR 0.015 0.002 TYR N 284 ARG 0.011 0.001 ARG 6 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 833 time to evaluate : 4.000 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: 1 79 MET cc_start: 0.8378 (mmm) cc_final: 0.7958 (mmm) REVERT: 1 97 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7630 (pt0) REVERT: 1 208 GLN cc_start: 0.7631 (mp10) cc_final: 0.7397 (pp30) REVERT: 1 342 TRP cc_start: 0.8500 (t-100) cc_final: 0.7858 (t60) REVERT: 2 28 MET cc_start: 0.7697 (mmm) cc_final: 0.6917 (tpt) REVERT: 2 89 LYS cc_start: 0.8651 (tptp) cc_final: 0.8221 (tptp) REVERT: 3 132 ASP cc_start: 0.9227 (m-30) cc_final: 0.8820 (m-30) REVERT: 3 200 LEU cc_start: 0.8985 (mm) cc_final: 0.8562 (mm) REVERT: 3 237 ASP cc_start: 0.8751 (t0) cc_final: 0.8472 (t0) REVERT: 3 239 THR cc_start: 0.8072 (m) cc_final: 0.7799 (p) REVERT: 3 426 TYR cc_start: 0.7099 (m-80) cc_final: 0.6420 (m-80) REVERT: 3 558 TRP cc_start: 0.6588 (p-90) cc_final: 0.6261 (p-90) REVERT: 4 78 ASN cc_start: 0.9185 (m-40) cc_final: 0.8235 (t0) REVERT: 4 130 LEU cc_start: 0.9288 (mm) cc_final: 0.8872 (mm) REVERT: 4 152 GLU cc_start: 0.7506 (mp0) cc_final: 0.7286 (mm-30) REVERT: 4 216 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6434 (tt0) REVERT: 4 230 ILE cc_start: 0.9016 (mt) cc_final: 0.8754 (mm) REVERT: 4 385 CYS cc_start: 0.8233 (t) cc_final: 0.7897 (t) REVERT: 5 122 PHE cc_start: 0.9159 (m-80) cc_final: 0.8917 (m-10) REVERT: 5 185 LYS cc_start: 0.8540 (pttt) cc_final: 0.8171 (pttt) REVERT: 6 177 LYS cc_start: 0.8142 (tmmt) cc_final: 0.6871 (tptp) REVERT: 9 12 ILE cc_start: 0.8752 (tp) cc_final: 0.8423 (tp) REVERT: 9 95 MET cc_start: 0.8840 (mmm) cc_final: 0.8054 (mmm) REVERT: 9 119 PHE cc_start: 0.8842 (p90) cc_final: 0.8427 (p90) REVERT: 7 91 ILE cc_start: 0.8472 (mm) cc_final: 0.8230 (mt) REVERT: 7 120 ASP cc_start: 0.7413 (t0) cc_final: 0.6529 (t0) REVERT: 7 121 ARG cc_start: 0.8040 (mpp80) cc_final: 0.7439 (mpp80) REVERT: A 11 LEU cc_start: 0.8592 (mt) cc_final: 0.8116 (tt) REVERT: A 57 PHE cc_start: 0.8475 (m-80) cc_final: 0.8044 (m-80) REVERT: A 81 TYR cc_start: 0.8572 (t80) cc_final: 0.7996 (t80) REVERT: J 47 ASP cc_start: 0.8820 (t0) cc_final: 0.7792 (t0) REVERT: J 55 GLN cc_start: 0.8804 (tp-100) cc_final: 0.8490 (tp40) REVERT: J 119 LEU cc_start: 0.9134 (mp) cc_final: 0.8648 (mp) REVERT: J 138 VAL cc_start: 0.9427 (t) cc_final: 0.9151 (t) REVERT: K 70 VAL cc_start: 0.9091 (m) cc_final: 0.8677 (p) REVERT: L 92 ILE cc_start: 0.6861 (mt) cc_final: 0.6526 (tt) REVERT: L 169 PHE cc_start: 0.8395 (t80) cc_final: 0.8166 (t80) REVERT: L 319 LEU cc_start: 0.8970 (mt) cc_final: 0.8742 (mm) REVERT: M 122 PHE cc_start: 0.8956 (t80) cc_final: 0.8721 (t80) REVERT: M 132 MET cc_start: 0.8965 (ptm) cc_final: 0.8607 (ptp) REVERT: M 135 LEU cc_start: 0.9180 (mt) cc_final: 0.8332 (tp) REVERT: M 204 LYS cc_start: 0.8626 (tppt) cc_final: 0.8152 (tppp) REVERT: M 251 GLU cc_start: 0.7619 (mp0) cc_final: 0.6597 (tp30) REVERT: M 357 LEU cc_start: 0.8955 (tp) cc_final: 0.8682 (tp) REVERT: N 35 LEU cc_start: 0.9173 (tp) cc_final: 0.8898 (tp) REVERT: N 135 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8618 (mttp) REVERT: N 251 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8799 (mm-40) REVERT: N 261 SER cc_start: 0.9165 (m) cc_final: 0.8739 (p) REVERT: N 345 LYS cc_start: 0.9222 (mttp) cc_final: 0.8697 (mttm) REVERT: N 420 LEU cc_start: 0.8637 (tp) cc_final: 0.8287 (tt) REVERT: H 79 ARG cc_start: 0.8019 (mmt180) cc_final: 0.6875 (ttp-170) REVERT: H 82 PHE cc_start: 0.8500 (t80) cc_final: 0.8287 (t80) REVERT: H 137 PHE cc_start: 0.8016 (p90) cc_final: 0.7795 (p90) REVERT: H 181 ASN cc_start: 0.8230 (m-40) cc_final: 0.7940 (t0) REVERT: H 189 GLN cc_start: 0.8531 (mp10) cc_final: 0.8080 (mp10) REVERT: H 277 LEU cc_start: 0.8337 (tp) cc_final: 0.8019 (mm) REVERT: H 328 VAL cc_start: 0.8610 (t) cc_final: 0.8347 (t) outliers start: 1 outliers final: 0 residues processed: 834 average time/residue: 0.4415 time to fit residues: 622.5210 Evaluate side-chains 661 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 661 time to evaluate : 3.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 269 optimal weight: 6.9990 chunk 434 optimal weight: 4.9990 chunk 264 optimal weight: 0.9980 chunk 205 optimal weight: 0.7980 chunk 301 optimal weight: 4.9990 chunk 455 optimal weight: 6.9990 chunk 419 optimal weight: 0.9980 chunk 362 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 280 optimal weight: 1.9990 chunk 222 optimal weight: 0.4980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 129 HIS ** 2 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 225 ASN ** 3 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 389 GLN ** 5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.258 37052 Z= 0.763 Angle : 2.245 50.779 50464 Z= 1.466 Chirality : 0.444 6.468 5664 Planarity : 0.005 0.060 6374 Dihedral : 5.919 168.134 5088 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.99 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.12), residues: 4612 helix: 0.65 (0.11), residues: 2424 sheet: -1.01 (0.31), residues: 287 loop : -1.62 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP L 316 HIS 0.033 0.001 HIS 2 177 PHE 0.033 0.002 PHE N 220 TYR 0.017 0.001 TYR N 90 ARG 0.009 0.000 ARG L 529 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 857 time to evaluate : 3.975 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: 1 79 MET cc_start: 0.8340 (mmm) cc_final: 0.7954 (mmm) REVERT: 1 97 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7562 (pt0) REVERT: 1 222 GLU cc_start: 0.8274 (tt0) cc_final: 0.7857 (tt0) REVERT: 1 342 TRP cc_start: 0.8585 (t-100) cc_final: 0.8095 (t60) REVERT: 2 78 TYR cc_start: 0.7927 (m-10) cc_final: 0.7558 (m-10) REVERT: 2 89 LYS cc_start: 0.8559 (tptp) cc_final: 0.7949 (tptp) REVERT: 3 47 MET cc_start: 0.8939 (tpt) cc_final: 0.8569 (mmt) REVERT: 3 132 ASP cc_start: 0.9212 (m-30) cc_final: 0.8756 (m-30) REVERT: 3 179 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8737 (mt-10) REVERT: 3 249 MET cc_start: 0.8621 (mmt) cc_final: 0.8156 (mmm) REVERT: 3 395 PHE cc_start: 0.8491 (t80) cc_final: 0.8104 (t80) REVERT: 3 426 TYR cc_start: 0.7273 (m-80) cc_final: 0.6403 (m-80) REVERT: 3 558 TRP cc_start: 0.6552 (p-90) cc_final: 0.6221 (p-90) REVERT: 4 93 HIS cc_start: 0.8410 (m-70) cc_final: 0.7926 (m-70) REVERT: 4 130 LEU cc_start: 0.9157 (mm) cc_final: 0.8738 (mm) REVERT: 4 216 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6504 (tt0) REVERT: 4 230 ILE cc_start: 0.8942 (mt) cc_final: 0.8637 (mm) REVERT: 4 385 CYS cc_start: 0.8164 (t) cc_final: 0.7935 (t) REVERT: 5 185 LYS cc_start: 0.8536 (pttt) cc_final: 0.8240 (pttt) REVERT: 6 113 SER cc_start: 0.9624 (m) cc_final: 0.9204 (p) REVERT: 6 114 SER cc_start: 0.8658 (p) cc_final: 0.8427 (p) REVERT: 6 117 MET cc_start: 0.8029 (pmm) cc_final: 0.7727 (pmm) REVERT: 6 177 LYS cc_start: 0.8219 (tmmt) cc_final: 0.6935 (tptp) REVERT: 9 12 ILE cc_start: 0.8713 (tp) cc_final: 0.8405 (tp) REVERT: 9 95 MET cc_start: 0.8826 (mmm) cc_final: 0.7978 (mmm) REVERT: 9 119 PHE cc_start: 0.8759 (p90) cc_final: 0.8281 (p90) REVERT: 7 55 MET cc_start: 0.7074 (ttt) cc_final: 0.6239 (ttt) REVERT: 7 91 ILE cc_start: 0.8462 (mm) cc_final: 0.8170 (mt) REVERT: A 11 LEU cc_start: 0.8696 (mt) cc_final: 0.8084 (tt) REVERT: A 57 PHE cc_start: 0.8387 (m-80) cc_final: 0.8030 (m-80) REVERT: A 75 VAL cc_start: 0.9182 (p) cc_final: 0.8795 (p) REVERT: A 81 TYR cc_start: 0.8448 (t80) cc_final: 0.7956 (t80) REVERT: J 5 GLU cc_start: 0.7127 (pp20) cc_final: 0.6446 (tp30) REVERT: J 47 ASP cc_start: 0.8796 (t0) cc_final: 0.7802 (t0) REVERT: J 83 PHE cc_start: 0.4405 (m-80) cc_final: 0.3248 (p90) REVERT: J 119 LEU cc_start: 0.9098 (mp) cc_final: 0.8669 (mp) REVERT: J 138 VAL cc_start: 0.9342 (t) cc_final: 0.8986 (t) REVERT: K 70 VAL cc_start: 0.9064 (m) cc_final: 0.8699 (p) REVERT: L 92 ILE cc_start: 0.6809 (mt) cc_final: 0.6468 (tt) REVERT: L 245 MET cc_start: 0.7716 (mmm) cc_final: 0.7437 (mmm) REVERT: L 308 LEU cc_start: 0.8203 (tp) cc_final: 0.7989 (tp) REVERT: M 132 MET cc_start: 0.8938 (ptm) cc_final: 0.8659 (ptp) REVERT: M 135 LEU cc_start: 0.9185 (mt) cc_final: 0.8418 (tp) REVERT: M 148 PHE cc_start: 0.8450 (t80) cc_final: 0.8230 (t80) REVERT: M 204 LYS cc_start: 0.8622 (tppt) cc_final: 0.8125 (tppp) REVERT: M 244 PHE cc_start: 0.8102 (m-80) cc_final: 0.7626 (m-10) REVERT: M 251 GLU cc_start: 0.7490 (mp0) cc_final: 0.6492 (tp30) REVERT: M 357 LEU cc_start: 0.8912 (tp) cc_final: 0.8655 (tp) REVERT: N 35 LEU cc_start: 0.9170 (tp) cc_final: 0.8867 (tp) REVERT: N 125 ARG cc_start: 0.5390 (mtm-85) cc_final: 0.5155 (mtm-85) REVERT: N 135 LYS cc_start: 0.8859 (mtmm) cc_final: 0.8544 (mttp) REVERT: N 216 LYS cc_start: 0.8796 (mmmt) cc_final: 0.8562 (mmtm) REVERT: N 345 LYS cc_start: 0.9222 (mttp) cc_final: 0.8746 (mttm) REVERT: N 418 LEU cc_start: 0.7779 (mp) cc_final: 0.7571 (mt) REVERT: N 420 LEU cc_start: 0.8623 (tp) cc_final: 0.8170 (tt) REVERT: H 16 LYS cc_start: 0.5656 (tttp) cc_final: 0.5444 (tttp) REVERT: H 33 LEU cc_start: 0.9460 (mm) cc_final: 0.8859 (tt) REVERT: H 35 GLU cc_start: 0.8901 (tt0) cc_final: 0.8632 (tt0) REVERT: H 64 ILE cc_start: 0.9202 (tp) cc_final: 0.8943 (mt) REVERT: H 79 ARG cc_start: 0.7982 (mmt180) cc_final: 0.6756 (ttp-170) REVERT: H 82 PHE cc_start: 0.8434 (t80) cc_final: 0.8231 (t80) REVERT: H 181 ASN cc_start: 0.8285 (m-40) cc_final: 0.7947 (t0) REVERT: H 186 VAL cc_start: 0.8813 (t) cc_final: 0.8130 (t) REVERT: H 189 GLN cc_start: 0.8701 (mp10) cc_final: 0.7892 (mp10) REVERT: H 302 TYR cc_start: 0.7701 (p90) cc_final: 0.7390 (p90) REVERT: H 328 VAL cc_start: 0.8595 (t) cc_final: 0.8324 (t) outliers start: 0 outliers final: 0 residues processed: 857 average time/residue: 0.4467 time to fit residues: 643.2713 Evaluate side-chains 678 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 678 time to evaluate : 4.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 287 optimal weight: 0.9980 chunk 386 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 334 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 363 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 372 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 129 HIS ** 2 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 177 HIS ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 225 ASN 3 286 ASN ** 3 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 166 GLN ** 4 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN L 582 GLN N 60 GLN ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.107050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.095176 restraints weight = 97015.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.096339 restraints weight = 61414.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.097681 restraints weight = 46908.031| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.257 37052 Z= 0.764 Angle : 2.245 50.786 50464 Z= 1.466 Chirality : 0.444 6.462 5664 Planarity : 0.005 0.060 6374 Dihedral : 5.863 168.894 5088 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.97 % Favored : 94.82 % Rotamer: Outliers : 0.05 % Allowed : 0.52 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.55 (0.12), residues: 4612 helix: 0.65 (0.11), residues: 2437 sheet: -0.97 (0.31), residues: 288 loop : -1.61 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP L 316 HIS 0.028 0.001 HIS 2 177 PHE 0.034 0.002 PHE A 99 TYR 0.030 0.001 TYR M 405 ARG 0.008 0.000 ARG 2 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11121.79 seconds wall clock time: 199 minutes 54.40 seconds (11994.40 seconds total)