Starting phenix.real_space_refine on Sun Feb 18 11:52:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4j_12720/02_2024/7o4j_12720_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4j_12720/02_2024/7o4j_12720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4j_12720/02_2024/7o4j_12720.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4j_12720/02_2024/7o4j_12720.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4j_12720/02_2024/7o4j_12720_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4j_12720/02_2024/7o4j_12720_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 10 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 17 6.06 5 P 92 5.49 5 Mg 2 5.21 5 S 401 5.16 5 Be 1 3.05 5 C 45955 2.51 5 N 12617 2.21 5 O 13933 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 67": "NH1" <-> "NH2" Residue "0 GLU 78": "OE1" <-> "OE2" Residue "0 GLU 80": "OE1" <-> "OE2" Residue "0 GLU 101": "OE1" <-> "OE2" Residue "0 ARG 104": "NH1" <-> "NH2" Residue "0 GLU 119": "OE1" <-> "OE2" Residue "0 GLU 131": "OE1" <-> "OE2" Residue "0 GLU 147": "OE1" <-> "OE2" Residue "0 GLU 186": "OE1" <-> "OE2" Residue "0 ARG 197": "NH1" <-> "NH2" Residue "0 GLU 225": "OE1" <-> "OE2" Residue "0 GLU 246": "OE1" <-> "OE2" Residue "0 ARG 270": "NH1" <-> "NH2" Residue "0 GLU 273": "OE1" <-> "OE2" Residue "0 GLU 285": "OE1" <-> "OE2" Residue "0 GLU 287": "OE1" <-> "OE2" Residue "0 GLU 304": "OE1" <-> "OE2" Residue "0 GLU 319": "OE1" <-> "OE2" Residue "0 PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 375": "NH1" <-> "NH2" Residue "0 ARG 380": "NH1" <-> "NH2" Residue "0 GLU 389": "OE1" <-> "OE2" Residue "0 GLU 394": "OE1" <-> "OE2" Residue "0 GLU 421": "OE1" <-> "OE2" Residue "0 TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 424": "OE1" <-> "OE2" Residue "0 GLU 451": "OE1" <-> "OE2" Residue "0 TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 509": "NH1" <-> "NH2" Residue "0 GLU 511": "OE1" <-> "OE2" Residue "0 ARG 520": "NH1" <-> "NH2" Residue "0 ARG 594": "NH1" <-> "NH2" Residue "0 GLU 608": "OE1" <-> "OE2" Residue "0 GLU 631": "OE1" <-> "OE2" Residue "0 ARG 638": "NH1" <-> "NH2" Residue "0 GLU 640": "OE1" <-> "OE2" Residue "0 GLU 650": "OE1" <-> "OE2" Residue "0 ARG 671": "NH1" <-> "NH2" Residue "0 ARG 685": "NH1" <-> "NH2" Residue "0 ARG 688": "NH1" <-> "NH2" Residue "0 ARG 722": "NH1" <-> "NH2" Residue "0 ARG 751": "NH1" <-> "NH2" Residue "1 ARG 30": "NH1" <-> "NH2" Residue "1 ARG 86": "NH1" <-> "NH2" Residue "1 ARG 110": "NH1" <-> "NH2" Residue "1 ARG 121": "NH1" <-> "NH2" Residue "1 GLU 172": "OE1" <-> "OE2" Residue "1 PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 253": "NH1" <-> "NH2" Residue "1 GLU 261": "OE1" <-> "OE2" Residue "1 PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 286": "NH1" <-> "NH2" Residue "1 GLU 392": "OE1" <-> "OE2" Residue "1 GLU 415": "OE1" <-> "OE2" Residue "1 ARG 416": "NH1" <-> "NH2" Residue "1 GLU 494": "OE1" <-> "OE2" Residue "1 ARG 502": "NH1" <-> "NH2" Residue "1 GLU 537": "OE1" <-> "OE2" Residue "1 GLU 548": "OE1" <-> "OE2" Residue "1 GLU 572": "OE1" <-> "OE2" Residue "1 GLU 595": "OE1" <-> "OE2" Residue "2 GLU 15": "OE1" <-> "OE2" Residue "2 ARG 24": "NH1" <-> "NH2" Residue "2 ARG 37": "NH1" <-> "NH2" Residue "2 GLU 54": "OE1" <-> "OE2" Residue "2 GLU 126": "OE1" <-> "OE2" Residue "2 GLU 144": "OE1" <-> "OE2" Residue "2 GLU 161": "OE1" <-> "OE2" Residue "2 GLU 174": "OE1" <-> "OE2" Residue "2 GLU 187": "OE1" <-> "OE2" Residue "2 GLU 195": "OE1" <-> "OE2" Residue "2 ARG 247": "NH1" <-> "NH2" Residue "2 ARG 254": "NH1" <-> "NH2" Residue "2 GLU 342": "OE1" <-> "OE2" Residue "2 TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 369": "NH1" <-> "NH2" Residue "2 ARG 380": "NH1" <-> "NH2" Residue "2 ARG 384": "NH1" <-> "NH2" Residue "2 ARG 385": "NH1" <-> "NH2" Residue "2 GLU 401": "OE1" <-> "OE2" Residue "2 GLU 447": "OE1" <-> "OE2" Residue "2 ARG 450": "NH1" <-> "NH2" Residue "2 PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 467": "OE1" <-> "OE2" Residue "2 PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 77": "OE1" <-> "OE2" Residue "3 GLU 105": "OE1" <-> "OE2" Residue "3 GLU 111": "OE1" <-> "OE2" Residue "3 GLU 130": "OE1" <-> "OE2" Residue "3 TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 42": "OE1" <-> "OE2" Residue "4 GLU 55": "OE1" <-> "OE2" Residue "4 ARG 119": "NH1" <-> "NH2" Residue "4 GLU 123": "OE1" <-> "OE2" Residue "4 ARG 146": "NH1" <-> "NH2" Residue "4 ARG 162": "NH1" <-> "NH2" Residue "4 GLU 166": "OE1" <-> "OE2" Residue "4 ARG 175": "NH1" <-> "NH2" Residue "4 GLU 239": "OE1" <-> "OE2" Residue "4 ARG 281": "NH1" <-> "NH2" Residue "6 GLU 134": "OE1" <-> "OE2" Residue "6 ARG 142": "NH1" <-> "NH2" Residue "6 GLU 275": "OE1" <-> "OE2" Residue "6 GLU 285": "OE1" <-> "OE2" Residue "6 GLU 303": "OE1" <-> "OE2" Residue "6 ARG 327": "NH1" <-> "NH2" Residue "6 GLU 330": "OE1" <-> "OE2" Residue "6 GLU 396": "OE1" <-> "OE2" Residue "6 ARG 409": "NH1" <-> "NH2" Residue "6 ARG 426": "NH1" <-> "NH2" Residue "6 ARG 428": "NH1" <-> "NH2" Residue "6 PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 455": "OE1" <-> "OE2" Residue "7 ARG 114": "NH1" <-> "NH2" Residue "7 ARG 122": "NH1" <-> "NH2" Residue "7 ARG 124": "NH1" <-> "NH2" Residue "7 ARG 140": "NH1" <-> "NH2" Residue "7 GLU 162": "OE1" <-> "OE2" Residue "7 GLU 189": "OE1" <-> "OE2" Residue "7 ARG 199": "NH1" <-> "NH2" Residue "7 GLU 324": "OE1" <-> "OE2" Residue "7 ARG 329": "NH1" <-> "NH2" Residue "7 ARG 344": "NH1" <-> "NH2" Residue "7 TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 378": "NH1" <-> "NH2" Residue "7 ARG 421": "NH1" <-> "NH2" Residue "7 GLU 433": "OE1" <-> "OE2" Residue "7 GLU 449": "OE1" <-> "OE2" Residue "7 ARG 480": "NH1" <-> "NH2" Residue "7 ARG 519": "NH1" <-> "NH2" Residue "7 PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 537": "OE1" <-> "OE2" Residue "7 ARG 571": "NH1" <-> "NH2" Residue "7 ARG 577": "NH1" <-> "NH2" Residue "7 TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 686": "NH1" <-> "NH2" Residue "7 ARG 692": "NH1" <-> "NH2" Residue "7 ARG 696": "NH1" <-> "NH2" Residue "7 GLU 762": "OE1" <-> "OE2" Residue "7 ARG 834": "NH1" <-> "NH2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A GLU 542": "OE1" <-> "OE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 801": "OE1" <-> "OE2" Residue "A GLU 812": "OE1" <-> "OE2" Residue "A GLU 833": "OE1" <-> "OE2" Residue "A GLU 931": "OE1" <-> "OE2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A ARG 961": "NH1" <-> "NH2" Residue "A GLU 995": "OE1" <-> "OE2" Residue "A ARG 1012": "NH1" <-> "NH2" Residue "A ARG 1100": "NH1" <-> "NH2" Residue "A GLU 1103": "OE1" <-> "OE2" Residue "A ARG 1159": "NH1" <-> "NH2" Residue "A GLU 1256": "OE1" <-> "OE2" Residue "A ARG 1281": "NH1" <-> "NH2" Residue "A GLU 1301": "OE1" <-> "OE2" Residue "A GLU 1307": "OE1" <-> "OE2" Residue "A GLU 1351": "OE1" <-> "OE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 348": "NH1" <-> "NH2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B GLU 598": "OE1" <-> "OE2" Residue "B GLU 612": "OE1" <-> "OE2" Residue "B GLU 678": "OE1" <-> "OE2" Residue "B GLU 714": "OE1" <-> "OE2" Residue "B GLU 810": "OE1" <-> "OE2" Residue "B GLU 816": "OE1" <-> "OE2" Residue "B PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B ARG 884": "NH1" <-> "NH2" Residue "B GLU 922": "OE1" <-> "OE2" Residue "B GLU 923": "OE1" <-> "OE2" Residue "B GLU 924": "OE1" <-> "OE2" Residue "B GLU 1041": "OE1" <-> "OE2" Residue "B ARG 1124": "NH1" <-> "NH2" Residue "B GLU 1206": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "F GLU 71": "OE1" <-> "OE2" Residue "F GLU 114": "OE1" <-> "OE2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 138": "OE1" <-> "OE2" Residue "H ARG 146": "NH1" <-> "NH2" Residue "I TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 21": "OE1" <-> "OE2" Residue "I GLU 28": "OE1" <-> "OE2" Residue "I ARG 30": "NH1" <-> "NH2" Residue "I TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I GLU 74": "OE1" <-> "OE2" Residue "J GLU 32": "OE1" <-> "OE2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 63": "NH1" <-> "NH2" Residue "M GLU 36": "OE1" <-> "OE2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "M ARG 95": "NH1" <-> "NH2" Residue "M GLU 152": "OE1" <-> "OE2" Residue "M GLU 169": "OE1" <-> "OE2" Residue "M GLU 184": "OE1" <-> "OE2" Residue "M GLU 191": "OE1" <-> "OE2" Residue "M GLU 268": "OE1" <-> "OE2" Residue "M GLU 318": "OE1" <-> "OE2" Residue "M ARG 320": "NH1" <-> "NH2" Residue "O ARG 79": "NH1" <-> "NH2" Residue "O GLU 93": "OE1" <-> "OE2" Residue "O GLU 129": "OE1" <-> "OE2" Residue "O ARG 141": "NH1" <-> "NH2" Residue "O PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 221": "OE1" <-> "OE2" Residue "O GLU 222": "OE1" <-> "OE2" Residue "Q ARG 28": "NH1" <-> "NH2" Residue "Q ARG 29": "NH1" <-> "NH2" Residue "Q GLU 97": "OE1" <-> "OE2" Residue "Q ARG 115": "NH1" <-> "NH2" Residue "Q ARG 138": "NH1" <-> "NH2" Residue "Q ARG 153": "NH1" <-> "NH2" Residue "Q GLU 162": "OE1" <-> "OE2" Residue "Q GLU 165": "OE1" <-> "OE2" Residue "Q TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 327": "NH1" <-> "NH2" Residue "Q GLU 353": "OE1" <-> "OE2" Residue "Q ARG 398": "NH1" <-> "NH2" Residue "Q GLU 408": "OE1" <-> "OE2" Residue "Q GLU 410": "OE1" <-> "OE2" Residue "Q ARG 412": "NH1" <-> "NH2" Residue "Q GLU 419": "OE1" <-> "OE2" Residue "Q ARG 422": "NH1" <-> "NH2" Residue "R GLU 38": "OE1" <-> "OE2" Residue "R ARG 63": "NH1" <-> "NH2" Residue "R GLU 79": "OE1" <-> "OE2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R GLU 91": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "R GLU 132": "OE1" <-> "OE2" Residue "R ARG 198": "NH1" <-> "NH2" Residue "R TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 238": "OE1" <-> "OE2" Residue "R ARG 240": "NH1" <-> "NH2" Residue "R ARG 251": "NH1" <-> "NH2" Residue "R ARG 271": "NH1" <-> "NH2" Residue "R GLU 298": "OE1" <-> "OE2" Residue "R GLU 320": "OE1" <-> "OE2" Residue "R ARG 323": "NH1" <-> "NH2" Residue "R GLU 326": "OE1" <-> "OE2" Residue "R ARG 352": "NH1" <-> "NH2" Residue "R GLU 354": "OE1" <-> "OE2" Residue "U ARG 8": "NH1" <-> "NH2" Residue "U GLU 20": "OE1" <-> "OE2" Residue "U ARG 22": "NH1" <-> "NH2" Residue "U GLU 32": "OE1" <-> "OE2" Residue "U GLU 48": "OE1" <-> "OE2" Residue "U ARG 271": "NH1" <-> "NH2" Residue "U GLU 282": "OE1" <-> "OE2" Residue "U GLU 284": "OE1" <-> "OE2" Residue "V ARG 11": "NH1" <-> "NH2" Residue "V ARG 39": "NH1" <-> "NH2" Residue "V GLU 42": "OE1" <-> "OE2" Residue "V GLU 50": "OE1" <-> "OE2" Residue "V TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 3": "NH1" <-> "NH2" Residue "W PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 18": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 65": "NH1" <-> "NH2" Residue "W ARG 108": "NH1" <-> "NH2" Residue "W ARG 144": "NH1" <-> "NH2" Residue "W GLU 146": "OE1" <-> "OE2" Residue "W GLU 196": "OE1" <-> "OE2" Residue "W GLU 200": "OE1" <-> "OE2" Residue "W ARG 205": "NH1" <-> "NH2" Residue "W ARG 274": "NH1" <-> "NH2" Residue "W ARG 279": "NH1" <-> "NH2" Residue "W GLU 283": "OE1" <-> "OE2" Residue "W ARG 285": "NH1" <-> "NH2" Residue "W GLU 292": "OE1" <-> "OE2" Residue "W ARG 351": "NH1" <-> "NH2" Residue "W GLU 352": "OE1" <-> "OE2" Residue "W GLU 410": "OE1" <-> "OE2" Residue "X GLU 133": "OE1" <-> "OE2" Residue "X GLU 161": "OE1" <-> "OE2" Residue "X ARG 168": "NH1" <-> "NH2" Residue "X ARG 197": "NH1" <-> "NH2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X ARG 234": "NH1" <-> "NH2" Residue "X GLU 258": "OE1" <-> "OE2" Residue "X GLU 264": "OE1" <-> "OE2" Residue "X GLU 273": "OE1" <-> "OE2" Residue "X ARG 276": "NH1" <-> "NH2" Residue "X TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 73025 Number of models: 1 Model: "" Number of chains: 43 Chain: "0" Number of atoms: 6091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6091 Classifications: {'peptide': 752} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 719} Chain: "1" Number of atoms: 4214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4214 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 503} Chain breaks: 6 Chain: "2" Number of atoms: 3597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3597 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 17, 'TRANS': 427} Chain breaks: 4 Chain: "3" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1089 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "4" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2274 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 279} Chain breaks: 2 Chain: "5" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "6" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2794 Classifications: {'peptide': 356} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 334} Chain breaks: 1 Chain: "7" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4954 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 24, 'TRANS': 590} Chain breaks: 2 Chain: "A" Number of atoms: 11254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1430, 11254 Classifications: {'peptide': 1430} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1363} Chain breaks: 3 Chain: "B" Number of atoms: 9404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9404 Classifications: {'peptide': 1180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1127} Chain breaks: 5 Chain: "C" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2092 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1343 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 697 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2360 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 295} Chain breaks: 2 Chain: "N" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 928 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1422 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 172} Chain: "Q" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1871 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain breaks: 2 Chain: "R" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2230 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain breaks: 1 Chain: "T" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 917 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "U" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 885 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 105} Chain breaks: 2 Chain: "V" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 815 Classifications: {'peptide': 104} Link IDs: {'TRANS': 103} Chain breaks: 1 Chain: "W" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2532 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 15, 'TRANS': 296} Chain breaks: 3 Chain: "X" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1683 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "7" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 938 SG CYS 0 115 79.499 88.766 187.627 1.00 58.65 S ATOM 1265 SG CYS 0 156 74.847 87.934 191.887 1.00 67.26 S ATOM 1080 SG CYS 0 133 76.329 94.046 189.966 1.00 66.26 S ATOM 1566 SG CYS 0 191 79.719 91.221 193.909 1.00 58.10 S ATOM 13941 SG CYS 3 13 62.185 119.674 143.052 1.00 80.84 S ATOM 13962 SG CYS 3 16 63.365 119.026 139.462 1.00 73.72 S ATOM 14157 SG CYS 3 39 64.899 121.868 141.390 1.00 84.80 S ATOM 14178 SG CYS 3 42 61.310 122.136 140.304 1.00 85.67 S ATOM 14110 SG CYS 3 34 55.849 124.534 152.300 1.00 91.39 S ATOM 14268 SG CYS 3 54 54.903 123.692 148.640 1.00 94.31 S ATOM 14306 SG CYS 3 59 52.241 123.323 151.391 1.00 98.33 S ATOM 16970 SG CYS 4 289 129.742 49.360 206.130 1.00 57.33 S ATOM 16989 SG CYS 4 292 133.342 49.979 207.148 1.00 57.95 S ATOM 17081 SG CYS 4 305 131.083 47.997 209.434 1.00 68.04 S ATOM 17099 SG CYS 4 308 130.488 51.719 209.011 1.00 67.12 S ATOM 19766 SG CYS 6 349 133.182 32.471 192.317 1.00 54.55 S ATOM 19787 SG CYS 6 352 131.152 30.048 190.082 1.00 62.20 S ATOM 19866 SG CYS 6 363 131.843 33.433 188.834 1.00 56.15 S ATOM 19885 SG CYS 6 366 129.587 33.081 191.918 1.00 59.59 S ATOM 20187 SG CYS 6 403 160.229 67.931 203.228 1.00 69.36 S ATOM 20210 SG CYS 6 406 162.133 66.851 200.176 1.00 61.88 S ATOM 20404 SG CYS 6 437 159.448 69.588 199.814 1.00 67.43 S ATOM 20425 SG CYS 6 440 158.533 66.026 200.270 1.00 63.34 S ATOM 20337 SG CYS 6 429 150.494 65.616 209.968 1.00 77.25 S ATOM 20360 SG CYS 6 432 153.759 64.351 211.434 1.00 78.20 S ATOM 20518 SG CYS 6 451 152.701 63.313 207.952 1.00 62.81 S ATOM 20535 SG CYS 6 454 150.851 61.933 210.955 1.00 68.38 S ATOM 19665 SG CYS 6 336 136.461 33.461 178.400 1.00 70.85 S ATOM 19677 SG CYS 6 338 135.363 36.249 180.803 1.00 67.64 S ATOM 19825 SG CYS 6 357 139.062 35.753 179.917 1.00 61.29 S ATOM 26347 SG CYS A 107 101.050 114.070 114.359 1.00 37.43 S ATOM 26371 SG CYS A 110 99.841 115.617 117.543 1.00 46.34 S ATOM 26676 SG CYS A 148 103.614 114.914 117.095 1.00 51.38 S ATOM 26814 SG CYS A 167 101.188 112.023 117.499 1.00 65.27 S ATOM 26042 SG CYS A 67 61.909 139.187 101.488 1.00 35.86 S ATOM 26064 SG CYS A 70 62.499 142.822 102.516 1.00 30.70 S ATOM 26117 SG CYS A 77 64.444 141.328 99.579 1.00 23.10 S ATOM 45691 SG CYS B1163 75.406 143.858 112.935 1.00 21.65 S ATOM 45709 SG CYS B1166 76.620 140.911 110.715 1.00 21.65 S ATOM 45834 SG CYS B1182 72.999 141.082 111.861 1.00 29.15 S ATOM 45853 SG CYS B1185 75.854 140.382 114.308 1.00 37.03 S ATOM 46838 SG CYS C 86 44.590 179.455 48.126 1.00 40.89 S ATOM 46855 SG CYS C 88 43.956 175.940 49.476 1.00 51.28 S ATOM 46888 SG CYS C 92 42.474 177.096 46.082 1.00 34.97 S ATOM 46911 SG CYS C 95 46.196 176.436 46.493 1.00 25.12 S ATOM 54581 SG CYS I 7 131.670 89.156 58.048 1.00 75.02 S ATOM 54606 SG CYS I 10 128.073 88.876 59.496 1.00 75.62 S ATOM 54772 SG CYS I 29 130.657 90.555 61.558 1.00 88.45 S ATOM 54796 SG CYS I 32 131.146 86.821 60.615 1.00 91.40 S ATOM 55123 SG CYS I 75 134.036 122.389 29.202 1.00 71.05 S ATOM 55145 SG CYS I 78 133.342 121.251 25.541 1.00 77.70 S ATOM 55361 SG CYS I 103 130.465 121.845 27.735 1.00 63.88 S ATOM 55381 SG CYS I 106 132.824 118.944 28.544 1.00 71.47 S ATOM 55526 SG CYS J 7 73.581 165.949 34.196 1.00 41.48 S ATOM 55549 SG CYS J 10 73.076 169.640 33.204 1.00 11.09 S ATOM 55829 SG CYS J 45 76.596 167.920 32.957 1.00 16.96 S ATOM 55835 SG CYS J 46 73.786 167.243 30.574 1.00 18.73 S ATOM 57015 SG CYS L 31 48.657 130.610 44.345 1.00 43.35 S ATOM 57035 SG CYS L 34 46.405 130.448 41.325 1.00 53.67 S ATOM 57139 SG CYS L 48 45.162 129.144 44.658 1.00 49.54 S ATOM 57162 SG CYS L 51 47.994 127.263 42.867 1.00 57.74 S ATOM 57406 SG CYS M 24 48.323 159.475 91.038 1.00 66.88 S ATOM 57428 SG CYS M 27 45.580 161.215 89.078 1.00 79.24 S ATOM 57572 SG CYS M 45 47.692 158.616 87.288 1.00 51.81 S ATOM 57591 SG CYS M 48 49.311 161.872 88.448 1.00 50.73 S ATOM 69762 SG CYS W 124 48.436 136.418 110.802 1.00 87.79 S ATOM 69783 SG CYS W 127 51.740 135.720 109.331 1.00 87.41 S ATOM 69968 SG CYS W 149 50.755 139.343 110.371 1.00 78.11 S ATOM 69988 SG CYS W 152 49.201 137.691 107.275 1.00 79.16 S Time building chain proxies: 26.94, per 1000 atoms: 0.37 Number of scatterers: 73025 At special positions: 0 Unit cell: (218.4, 228.9, 238.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 17 29.99 Fe 4 26.01 S 401 16.00 P 92 15.00 Mg 2 11.99 F 3 9.00 O 13933 8.00 N 12617 7.00 C 45955 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.52 Conformation dependent library (CDL) restraints added in 9.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 42 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 16 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" ND1 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 54 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 352 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 440 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 403 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 454 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " Number of angles added : 93 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 349 helices and 73 sheets defined 39.4% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.92 Creating SS restraints... Processing helix chain '0' and resid 19 through 34 Processing helix chain '0' and resid 49 through 62 Processing helix chain '0' and resid 76 through 96 Processing helix chain '0' and resid 111 through 113 No H-bonds generated for 'chain '0' and resid 111 through 113' Processing helix chain '0' and resid 126 through 137 Processing helix chain '0' and resid 140 through 147 Processing helix chain '0' and resid 157 through 164 removed outlier: 3.690A pdb=" N LEU 0 162 " --> pdb=" O TYR 0 158 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR 0 163 " --> pdb=" O HIS 0 159 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN 0 164 " --> pdb=" O GLU 0 160 " (cutoff:3.500A) Processing helix chain '0' and resid 167 through 169 No H-bonds generated for 'chain '0' and resid 167 through 169' Processing helix chain '0' and resid 178 through 188 Processing helix chain '0' and resid 192 through 197 Processing helix chain '0' and resid 200 through 202 No H-bonds generated for 'chain '0' and resid 200 through 202' Processing helix chain '0' and resid 210 through 214 removed outlier: 4.122A pdb=" N LEU 0 214 " --> pdb=" O HIS 0 211 " (cutoff:3.500A) Processing helix chain '0' and resid 216 through 223 removed outlier: 3.739A pdb=" N GLU 0 220 " --> pdb=" O PRO 0 216 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ARG 0 221 " --> pdb=" O LYS 0 217 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL 0 222 " --> pdb=" O ILE 0 218 " (cutoff:3.500A) Processing helix chain '0' and resid 240 through 248 removed outlier: 4.342A pdb=" N LEU 0 248 " --> pdb=" O CYS 0 244 " (cutoff:3.500A) Processing helix chain '0' and resid 254 through 277 removed outlier: 3.849A pdb=" N ARG 0 262 " --> pdb=" O ARG 0 258 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL 0 277 " --> pdb=" O GLU 0 273 " (cutoff:3.500A) Processing helix chain '0' and resid 280 through 291 Processing helix chain '0' and resid 295 through 298 No H-bonds generated for 'chain '0' and resid 295 through 298' Processing helix chain '0' and resid 313 through 315 No H-bonds generated for 'chain '0' and resid 313 through 315' Processing helix chain '0' and resid 328 through 346 Processing helix chain '0' and resid 356 through 366 Processing helix chain '0' and resid 371 through 388 removed outlier: 3.601A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N SER 0 378 " --> pdb=" O LEU 0 374 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU 0 383 " --> pdb=" O GLU 0 379 " (cutoff:3.500A) Processing helix chain '0' and resid 395 through 409 removed outlier: 4.200A pdb=" N ALA 0 398 " --> pdb=" O ASP 0 395 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA 0 403 " --> pdb=" O LYS 0 400 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE 0 409 " --> pdb=" O ALA 0 406 " (cutoff:3.500A) Processing helix chain '0' and resid 444 through 452 Proline residue: 0 448 - end of helix Processing helix chain '0' and resid 467 through 472 Processing helix chain '0' and resid 510 through 512 No H-bonds generated for 'chain '0' and resid 510 through 512' Processing helix chain '0' and resid 516 through 532 removed outlier: 3.624A pdb=" N ILE 0 532 " --> pdb=" O GLU 0 528 " (cutoff:3.500A) Processing helix chain '0' and resid 544 through 557 Processing helix chain '0' and resid 559 through 566 removed outlier: 3.672A pdb=" N LYS 0 565 " --> pdb=" O ASP 0 561 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N HIS 0 566 " --> pdb=" O GLU 0 562 " (cutoff:3.500A) Processing helix chain '0' and resid 576 through 591 Processing helix chain '0' and resid 606 through 608 No H-bonds generated for 'chain '0' and resid 606 through 608' Processing helix chain '0' and resid 633 through 645 Processing helix chain '0' and resid 650 through 669 removed outlier: 3.552A pdb=" N HIS 0 661 " --> pdb=" O ASP 0 657 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG 0 668 " --> pdb=" O GLN 0 664 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N VAL 0 669 " --> pdb=" O CYS 0 665 " (cutoff:3.500A) Processing helix chain '0' and resid 684 through 688 removed outlier: 3.541A pdb=" N SER 0 687 " --> pdb=" O ARG 0 684 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG 0 688 " --> pdb=" O ARG 0 685 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 684 through 688' Processing helix chain '0' and resid 690 through 692 No H-bonds generated for 'chain '0' and resid 690 through 692' Processing helix chain '0' and resid 695 through 698 No H-bonds generated for 'chain '0' and resid 695 through 698' Processing helix chain '0' and resid 703 through 705 No H-bonds generated for 'chain '0' and resid 703 through 705' Processing helix chain '0' and resid 710 through 725 Processing helix chain '0' and resid 730 through 733 Processing helix chain '0' and resid 741 through 751 Processing helix chain '1' and resid 42 through 44 No H-bonds generated for 'chain '1' and resid 42 through 44' Processing helix chain '1' and resid 94 through 120 removed outlier: 3.756A pdb=" N THR 1 103 " --> pdb=" O ASN 1 99 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN 1 106 " --> pdb=" O MET 1 102 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE 1 107 " --> pdb=" O THR 1 103 " (cutoff:3.500A) Processing helix chain '1' and resid 171 through 176 Processing helix chain '1' and resid 178 through 187 removed outlier: 3.547A pdb=" N GLY 1 187 " --> pdb=" O SER 1 183 " (cutoff:3.500A) Processing helix chain '1' and resid 189 through 199 removed outlier: 3.580A pdb=" N GLU 1 197 " --> pdb=" O LYS 1 193 " (cutoff:3.500A) Processing helix chain '1' and resid 206 through 224 removed outlier: 4.240A pdb=" N THR 1 212 " --> pdb=" O GLU 1 208 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG 1 213 " --> pdb=" O PHE 1 209 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE 1 214 " --> pdb=" O TRP 1 210 " (cutoff:3.500A) Proline residue: 1 215 - end of helix removed outlier: 4.260A pdb=" N THR 1 224 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 233 through 236 No H-bonds generated for 'chain '1' and resid 233 through 236' Processing helix chain '1' and resid 253 through 262 Processing helix chain '1' and resid 264 through 271 Processing helix chain '1' and resid 280 through 289 removed outlier: 3.566A pdb=" N SER 1 289 " --> pdb=" O ALA 1 285 " (cutoff:3.500A) Processing helix chain '1' and resid 291 through 296 Processing helix chain '1' and resid 309 through 329 removed outlier: 3.906A pdb=" N ARG 1 313 " --> pdb=" O VAL 1 309 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TYR 1 314 " --> pdb=" O ILE 1 310 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU 1 315 " --> pdb=" O ILE 1 311 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR 1 316 " --> pdb=" O ASP 1 312 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU 1 317 " --> pdb=" O ARG 1 313 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG 1 323 " --> pdb=" O GLN 1 319 " (cutoff:3.500A) Processing helix chain '1' and resid 335 through 337 No H-bonds generated for 'chain '1' and resid 335 through 337' Processing helix chain '1' and resid 339 through 343 removed outlier: 3.616A pdb=" N ILE 1 343 " --> pdb=" O LEU 1 339 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 339 through 343' Processing helix chain '1' and resid 356 through 358 No H-bonds generated for 'chain '1' and resid 356 through 358' Processing helix chain '1' and resid 371 through 389 Processing helix chain '1' and resid 414 through 419 removed outlier: 3.557A pdb=" N GLU 1 418 " --> pdb=" O ASP 1 414 " (cutoff:3.500A) Processing helix chain '1' and resid 422 through 424 No H-bonds generated for 'chain '1' and resid 422 through 424' Processing helix chain '1' and resid 466 through 482 Processing helix chain '1' and resid 487 through 489 No H-bonds generated for 'chain '1' and resid 487 through 489' Processing helix chain '1' and resid 496 through 516 removed outlier: 3.641A pdb=" N ILE 1 509 " --> pdb=" O THR 1 505 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N HIS 1 516 " --> pdb=" O LYS 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 544 through 568 Processing helix chain '1' and resid 573 through 604 removed outlier: 4.748A pdb=" N SER 1 577 " --> pdb=" O LYS 1 574 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN 1 602 " --> pdb=" O ASP 1 599 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP 1 604 " --> pdb=" O LEU 1 601 " (cutoff:3.500A) Processing helix chain '1' and resid 609 through 615 Processing helix chain '1' and resid 617 through 638 Processing helix chain '2' and resid 6 through 16 Processing helix chain '2' and resid 19 through 26 removed outlier: 3.943A pdb=" N ARG 2 24 " --> pdb=" O GLN 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 38 removed outlier: 3.942A pdb=" N ARG 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE 2 38 " --> pdb=" O ALA 2 34 " (cutoff:3.500A) Processing helix chain '2' and resid 41 through 51 Processing helix chain '2' and resid 59 through 65 removed outlier: 3.605A pdb=" N TRP 2 65 " --> pdb=" O ASP 2 61 " (cutoff:3.500A) Processing helix chain '2' and resid 69 through 83 removed outlier: 4.538A pdb=" N LEU 2 72 " --> pdb=" O ASN 2 69 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA 2 77 " --> pdb=" O PHE 2 74 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE 2 78 " --> pdb=" O GLN 2 75 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER 2 80 " --> pdb=" O ALA 2 77 " (cutoff:3.500A) Processing helix chain '2' and resid 102 through 113 Processing helix chain '2' and resid 135 through 151 Processing helix chain '2' and resid 161 through 169 Processing helix chain '2' and resid 186 through 192 Processing helix chain '2' and resid 196 through 210 removed outlier: 3.922A pdb=" N LEU 2 203 " --> pdb=" O GLN 2 199 " (cutoff:3.500A) Processing helix chain '2' and resid 218 through 230 removed outlier: 3.540A pdb=" N MET 2 227 " --> pdb=" O HIS 2 223 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA 2 230 " --> pdb=" O PHE 2 226 " (cutoff:3.500A) Processing helix chain '2' and resid 245 through 256 removed outlier: 3.701A pdb=" N ASP 2 255 " --> pdb=" O GLN 2 251 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR 2 256 " --> pdb=" O ASP 2 252 " (cutoff:3.500A) Processing helix chain '2' and resid 273 through 276 No H-bonds generated for 'chain '2' and resid 273 through 276' Processing helix chain '2' and resid 354 through 362 Processing helix chain '2' and resid 380 through 389 removed outlier: 3.510A pdb=" N ASN 2 389 " --> pdb=" O ARG 2 385 " (cutoff:3.500A) Processing helix chain '2' and resid 393 through 402 Processing helix chain '2' and resid 406 through 422 Processing helix chain '2' and resid 435 through 448 Processing helix chain '2' and resid 465 through 477 Processing helix chain '2' and resid 495 through 506 removed outlier: 4.696A pdb=" N SER 2 499 " --> pdb=" O GLU 2 496 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN 2 500 " --> pdb=" O GLY 2 497 " (cutoff:3.500A) Processing helix chain '3' and resid 40 through 47 removed outlier: 3.607A pdb=" N ARG 3 45 " --> pdb=" O SER 3 41 " (cutoff:3.500A) Processing helix chain '3' and resid 65 through 67 No H-bonds generated for 'chain '3' and resid 65 through 67' Processing helix chain '3' and resid 76 through 89 Processing helix chain '3' and resid 96 through 99 Processing helix chain '3' and resid 103 through 122 Processing helix chain '3' and resid 126 through 138 removed outlier: 3.847A pdb=" N GLU 3 138 " --> pdb=" O ARG 3 134 " (cutoff:3.500A) Processing helix chain '4' and resid 34 through 43 removed outlier: 3.519A pdb=" N THR 4 39 " --> pdb=" O LYS 4 35 " (cutoff:3.500A) Processing helix chain '4' and resid 49 through 67 Processing helix chain '4' and resid 116 through 138 removed outlier: 3.533A pdb=" N VAL 4 121 " --> pdb=" O ARG 4 117 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR 4 124 " --> pdb=" O ASN 4 120 " (cutoff:3.500A) Processing helix chain '4' and resid 149 through 166 Processing helix chain '4' and resid 190 through 205 removed outlier: 3.990A pdb=" N ILE 4 194 " --> pdb=" O PHE 4 191 " (cutoff:3.500A) Proline residue: 4 195 - end of helix removed outlier: 3.624A pdb=" N PHE 4 201 " --> pdb=" O ASN 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 222 through 231 Processing helix chain '4' and resid 244 through 250 Processing helix chain '4' and resid 256 through 261 removed outlier: 3.535A pdb=" N ARG 4 259 " --> pdb=" O PRO 4 256 " (cutoff:3.500A) Proline residue: 4 260 - end of helix No H-bonds generated for 'chain '4' and resid 256 through 261' Processing helix chain '4' and resid 301 through 303 No H-bonds generated for 'chain '4' and resid 301 through 303' Processing helix chain '4' and resid 314 through 321 removed outlier: 3.688A pdb=" N LEU 4 320 " --> pdb=" O VAL 4 316 " (cutoff:3.500A) Processing helix chain '5' and resid 14 through 26 Processing helix chain '5' and resid 28 through 30 No H-bonds generated for 'chain '5' and resid 28 through 30' Processing helix chain '5' and resid 44 through 61 removed outlier: 4.501A pdb=" N GLU 5 48 " --> pdb=" O PRO 5 44 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE 5 49 " --> pdb=" O SER 5 45 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS 5 52 " --> pdb=" O GLU 5 48 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG 5 56 " --> pdb=" O HIS 5 52 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS 5 60 " --> pdb=" O ARG 5 56 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN 5 61 " --> pdb=" O LEU 5 57 " (cutoff:3.500A) Processing helix chain '6' and resid 97 through 113 removed outlier: 3.813A pdb=" N ALA 6 111 " --> pdb=" O LYS 6 107 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS 6 112 " --> pdb=" O LYS 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 137 Processing helix chain '6' and resid 145 through 163 Processing helix chain '6' and resid 189 through 199 Processing helix chain '6' and resid 210 through 220 Processing helix chain '6' and resid 247 through 256 Processing helix chain '6' and resid 271 through 279 Processing helix chain '6' and resid 294 through 305 removed outlier: 3.515A pdb=" N GLU 6 299 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA 6 304 " --> pdb=" O LEU 6 300 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL 6 305 " --> pdb=" O PHE 6 301 " (cutoff:3.500A) Processing helix chain '6' and resid 373 through 382 removed outlier: 4.476A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR 6 380 " --> pdb=" O LEU 6 376 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS 6 381 " --> pdb=" O ALA 6 377 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N HIS 6 382 " --> pdb=" O ARG 6 378 " (cutoff:3.500A) Processing helix chain '6' and resid 438 through 446 removed outlier: 3.867A pdb=" N VAL 6 442 " --> pdb=" O VAL 6 438 " (cutoff:3.500A) Processing helix chain '6' and resid 452 through 456 Processing helix chain '7' and resid 110 through 112 No H-bonds generated for 'chain '7' and resid 110 through 112' Processing helix chain '7' and resid 150 through 160 removed outlier: 3.801A pdb=" N ASP 7 155 " --> pdb=" O GLU 7 151 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE 7 156 " --> pdb=" O GLN 7 152 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL 7 158 " --> pdb=" O GLN 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 177 through 183 Processing helix chain '7' and resid 190 through 200 Processing helix chain '7' and resid 207 through 216 removed outlier: 3.612A pdb=" N ALA 7 216 " --> pdb=" O PHE 7 212 " (cutoff:3.500A) Processing helix chain '7' and resid 240 through 245 removed outlier: 3.602A pdb=" N LEU 7 245 " --> pdb=" O LEU 7 242 " (cutoff:3.500A) Processing helix chain '7' and resid 321 through 332 removed outlier: 4.119A pdb=" N GLU 7 324 " --> pdb=" O GLU 7 321 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS 7 327 " --> pdb=" O GLU 7 324 " (cutoff:3.500A) Processing helix chain '7' and resid 343 through 345 No H-bonds generated for 'chain '7' and resid 343 through 345' Processing helix chain '7' and resid 364 through 373 Processing helix chain '7' and resid 392 through 403 Processing helix chain '7' and resid 414 through 427 Processing helix chain '7' and resid 432 through 434 No H-bonds generated for 'chain '7' and resid 432 through 434' Processing helix chain '7' and resid 457 through 460 No H-bonds generated for 'chain '7' and resid 457 through 460' Processing helix chain '7' and resid 468 through 479 removed outlier: 3.618A pdb=" N LYS 7 472 " --> pdb=" O HIS 7 468 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL 7 473 " --> pdb=" O ASP 7 469 " (cutoff:3.500A) Processing helix chain '7' and resid 490 through 492 No H-bonds generated for 'chain '7' and resid 490 through 492' Processing helix chain '7' and resid 498 through 504 Processing helix chain '7' and resid 523 through 530 Processing helix chain '7' and resid 540 through 545 Processing helix chain '7' and resid 563 through 571 removed outlier: 4.162A pdb=" N GLU 7 568 " --> pdb=" O GLU 7 564 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR 7 569 " --> pdb=" O PHE 7 565 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU 7 570 " --> pdb=" O TYR 7 566 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG 7 571 " --> pdb=" O GLN 7 567 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 582 removed outlier: 3.592A pdb=" N MET 7 578 " --> pdb=" O ALA 7 574 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU 7 579 " --> pdb=" O ARG 7 575 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 600 Processing helix chain '7' and resid 612 through 622 Processing helix chain '7' and resid 633 through 645 Processing helix chain '7' and resid 656 through 659 Processing helix chain '7' and resid 680 through 689 removed outlier: 3.587A pdb=" N ALA 7 684 " --> pdb=" O ARG 7 680 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG 7 689 " --> pdb=" O GLN 7 685 " (cutoff:3.500A) Processing helix chain '7' and resid 714 through 722 Processing helix chain '7' and resid 724 through 729 removed outlier: 3.557A pdb=" N ASP 7 728 " --> pdb=" O ALA 7 724 " (cutoff:3.500A) Processing helix chain '7' and resid 753 through 766 removed outlier: 3.691A pdb=" N LYS 7 766 " --> pdb=" O GLU 7 762 " (cutoff:3.500A) Processing helix chain '7' and resid 832 through 836 removed outlier: 3.793A pdb=" N LYS 7 835 " --> pdb=" O LEU 7 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 93 through 105 removed outlier: 3.943A pdb=" N ILE A 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 131 through 144 removed outlier: 4.999A pdb=" N THR A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 211 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 286 through 304 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 472 through 478 removed outlier: 4.391A pdb=" N SER A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 534 removed outlier: 3.506A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.654A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 639 through 660 Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 673 through 698 Processing helix chain 'A' and resid 710 through 736 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 794 through 797 No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'A' and resid 810 through 844 Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 923 through 946 Processing helix chain 'A' and resid 960 through 971 Processing helix chain 'A' and resid 983 through 996 removed outlier: 3.742A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1025 removed outlier: 3.571A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1033 Processing helix chain 'A' and resid 1039 through 1056 Processing helix chain 'A' and resid 1064 through 1078 Proline residue: A1075 - end of helix removed outlier: 3.889A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1105 Processing helix chain 'A' and resid 1129 through 1138 Processing helix chain 'A' and resid 1143 through 1146 Processing helix chain 'A' and resid 1165 through 1176 removed outlier: 4.553A pdb=" N ILE A1170 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS A1173 " --> pdb=" O ILE A1170 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE A1174 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1204 Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1256 through 1269 Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 3.795A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1338 Processing helix chain 'A' and resid 1341 through 1359 removed outlier: 4.240A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1376 Processing helix chain 'A' and resid 1389 through 1391 No H-bonds generated for 'chain 'A' and resid 1389 through 1391' Processing helix chain 'A' and resid 1396 through 1401 removed outlier: 3.871A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1415 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 4.061A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 58 through 63 Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 308 through 320 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.931A pdb=" N ARG B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 358 Processing helix chain 'B' and resid 371 through 389 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 437 Processing helix chain 'B' and resid 444 through 447 No H-bonds generated for 'chain 'B' and resid 444 through 447' Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 488 through 496 removed outlier: 3.566A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 655 through 667 Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'B' and resid 697 through 700 Processing helix chain 'B' and resid 745 through 748 Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 764 through 776 removed outlier: 4.193A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 812 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 996 through 998 No H-bonds generated for 'chain 'B' and resid 996 through 998' Processing helix chain 'B' and resid 1014 through 1018 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1023 through 1038 Processing helix chain 'B' and resid 1052 through 1062 Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1122 through 1124 No H-bonds generated for 'chain 'B' and resid 1122 through 1124' Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1144 through 1152 Processing helix chain 'B' and resid 1198 through 1209 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 69 Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.620A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 267 removed outlier: 3.558A pdb=" N GLN C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' Processing helix chain 'D' and resid 52 through 72 removed outlier: 3.517A pdb=" N GLU D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 139 through 150 removed outlier: 3.628A pdb=" N ASN D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 removed outlier: 4.953A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 196 through 198 No H-bonds generated for 'chain 'D' and resid 196 through 198' Processing helix chain 'D' and resid 204 through 216 removed outlier: 3.537A pdb=" N ARG D 209 " --> pdb=" O ASP D 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 55 through 58 No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 102 Processing helix chain 'E' and resid 118 through 123 removed outlier: 4.730A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 167 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 33 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'H' and resid 89 through 92 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 44 through 51 removed outlier: 3.581A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 62 removed outlier: 3.722A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 Processing helix chain 'K' and resid 40 through 52 removed outlier: 3.577A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 3.810A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 120 through 139 removed outlier: 3.615A pdb=" N GLU M 125 " --> pdb=" O LYS M 121 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 157 Processing helix chain 'M' and resid 168 through 182 Processing helix chain 'M' and resid 189 through 193 Processing helix chain 'M' and resid 200 through 219 Processing helix chain 'M' and resid 228 through 230 No H-bonds generated for 'chain 'M' and resid 228 through 230' Processing helix chain 'M' and resid 235 through 246 removed outlier: 3.545A pdb=" N ILE M 239 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Proline residue: M 240 - end of helix removed outlier: 3.670A pdb=" N CYS M 243 " --> pdb=" O PRO M 240 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 265 removed outlier: 3.961A pdb=" N LYS M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLU M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 270 No H-bonds generated for 'chain 'M' and resid 267 through 270' Processing helix chain 'M' and resid 274 through 288 Processing helix chain 'M' and resid 295 through 301 Processing helix chain 'M' and resid 306 through 317 removed outlier: 3.683A pdb=" N ILE M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 323 No H-bonds generated for 'chain 'M' and resid 320 through 323' Processing helix chain 'M' and resid 326 through 331 Processing helix chain 'M' and resid 336 through 338 No H-bonds generated for 'chain 'M' and resid 336 through 338' Processing helix chain 'O' and resid 82 through 88 Processing helix chain 'O' and resid 129 through 146 removed outlier: 3.597A pdb=" N LYS O 133 " --> pdb=" O GLU O 129 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 178 Processing helix chain 'O' and resid 220 through 237 removed outlier: 3.617A pdb=" N TYR O 224 " --> pdb=" O ARG O 220 " (cutoff:3.500A) Proline residue: O 232 - end of helix removed outlier: 3.865A pdb=" N PHE O 237 " --> pdb=" O VAL O 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 34 Processing helix chain 'Q' and resid 108 through 110 No H-bonds generated for 'chain 'Q' and resid 108 through 110' Processing helix chain 'Q' and resid 153 through 167 Processing helix chain 'Q' and resid 337 through 345 Processing helix chain 'Q' and resid 406 through 413 Processing helix chain 'Q' and resid 424 through 431 Processing helix chain 'Q' and resid 437 through 449 removed outlier: 3.801A pdb=" N LYS Q 444 " --> pdb=" O ARG Q 440 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 52 No H-bonds generated for 'chain 'R' and resid 49 through 52' Processing helix chain 'R' and resid 75 through 81 removed outlier: 4.149A pdb=" N LYS R 80 " --> pdb=" O PHE R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 112 No H-bonds generated for 'chain 'R' and resid 110 through 112' Processing helix chain 'R' and resid 235 through 245 removed outlier: 3.932A pdb=" N VAL R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 265 removed outlier: 4.907A pdb=" N HIS R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 285 Processing helix chain 'R' and resid 296 through 309 removed outlier: 4.076A pdb=" N ASP R 301 " --> pdb=" O LYS R 297 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE R 304 " --> pdb=" O LEU R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 322 Processing helix chain 'R' and resid 326 through 336 removed outlier: 3.686A pdb=" N GLU R 331 " --> pdb=" O ALA R 327 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS R 332 " --> pdb=" O HIS R 328 " (cutoff:3.500A) Processing helix chain 'R' and resid 353 through 356 No H-bonds generated for 'chain 'R' and resid 353 through 356' Processing helix chain 'U' and resid 4 through 28 removed outlier: 3.686A pdb=" N ARG U 22 " --> pdb=" O VAL U 18 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLU U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP U 24 " --> pdb=" O GLU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 49 Processing helix chain 'V' and resid 9 through 12 Processing helix chain 'V' and resid 14 through 29 Processing helix chain 'V' and resid 34 through 54 removed outlier: 3.568A pdb=" N LYS V 46 " --> pdb=" O GLU V 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 20 Processing helix chain 'W' and resid 23 through 34 removed outlier: 3.517A pdb=" N LEU W 27 " --> pdb=" O GLY W 23 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 47 Processing helix chain 'W' and resid 51 through 63 Proline residue: W 56 - end of helix Processing helix chain 'W' and resid 91 through 116 Processing helix chain 'W' and resid 133 through 138 removed outlier: 3.535A pdb=" N VAL W 137 " --> pdb=" O GLN W 133 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN W 138 " --> pdb=" O LEU W 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 133 through 138' Processing helix chain 'W' and resid 163 through 178 removed outlier: 3.768A pdb=" N LYS W 166 " --> pdb=" O LYS W 163 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS W 168 " --> pdb=" O ASN W 165 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET W 176 " --> pdb=" O ASN W 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 191 Processing helix chain 'W' and resid 199 through 205 removed outlier: 3.672A pdb=" N ALA W 204 " --> pdb=" O GLU W 200 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG W 205 " --> pdb=" O ILE W 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 267 through 288 removed outlier: 3.602A pdb=" N ASN W 288 " --> pdb=" O LYS W 284 " (cutoff:3.500A) Processing helix chain 'W' and resid 350 through 368 Processing helix chain 'X' and resid 107 through 115 Processing helix chain 'X' and resid 124 through 136 Processing helix chain 'X' and resid 144 through 150 Processing helix chain 'X' and resid 158 through 165 Processing helix chain 'X' and resid 189 through 197 Processing helix chain 'X' and resid 207 through 211 Processing helix chain 'X' and resid 218 through 227 Processing helix chain 'X' and resid 257 through 265 removed outlier: 3.812A pdb=" N MET X 262 " --> pdb=" O GLU X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 271 through 280 Proline residue: X 275 - end of helix Processing helix chain 'X' and resid 290 through 292 No H-bonds generated for 'chain 'X' and resid 290 through 292' Processing sheet with id= A, first strand: chain '0' and resid 2 through 4 Processing sheet with id= B, first strand: chain '0' and resid 174 through 176 removed outlier: 4.105A pdb=" N GLY 0 107 " --> pdb=" O PHE 0 176 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE 0 205 " --> pdb=" O LEU 0 106 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE 0 69 " --> pdb=" O ILE 0 206 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N TYR 0 208 " --> pdb=" O ILE 0 69 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR 0 71 " --> pdb=" O TYR 0 208 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE 0 231 " --> pdb=" O ILE 0 70 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N CYS 0 72 " --> pdb=" O ILE 0 231 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE 0 233 " --> pdb=" O CYS 0 72 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE 0 39 " --> pdb=" O VAL 0 478 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN 0 480 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU 0 41 " --> pdb=" O GLN 0 480 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER 0 482 " --> pdb=" O GLU 0 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '0' and resid 250 through 253 Processing sheet with id= D, first strand: chain '0' and resid 492 through 497 removed outlier: 7.168A pdb=" N GLY 0 677 " --> pdb=" O LEU 0 493 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N MET 0 495 " --> pdb=" O GLY 0 677 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N MET 0 679 " --> pdb=" O MET 0 495 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE 0 497 " --> pdb=" O MET 0 679 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU 0 681 " --> pdb=" O ILE 0 497 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLY 0 536 " --> pdb=" O THR 0 619 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N LEU 0 621 " --> pdb=" O GLY 0 536 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL 0 538 " --> pdb=" O LEU 0 621 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ILE 0 623 " --> pdb=" O VAL 0 538 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE 0 540 " --> pdb=" O ILE 0 623 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA 0 596 " --> pdb=" O MET 0 537 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL 0 539 " --> pdb=" O ALA 0 596 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU 0 598 " --> pdb=" O VAL 0 539 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N PHE 0 541 " --> pdb=" O LEU 0 598 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER 0 600 " --> pdb=" O PHE 0 541 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU 0 568 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 568 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU 0 570 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 4 through 9 Processing sheet with id= F, first strand: chain '1' and resid 86 through 90 removed outlier: 3.832A pdb=" N LYS 1 47 " --> pdb=" O ILE 1 63 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '2' and resid 87 through 92 Processing sheet with id= H, first strand: chain '2' and resid 259 through 261 Processing sheet with id= I, first strand: chain '2' and resid 339 through 341 removed outlier: 6.162A pdb=" N GLN 2 377 " --> pdb=" O LEU 2 366 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU 2 366 " --> pdb=" O GLN 2 377 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '2' and resid 456 through 459 removed outlier: 6.361A pdb=" N SER 2 494 " --> pdb=" O LEU 2 481 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU 2 481 " --> pdb=" O SER 2 494 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '4' and resid 82 through 87 removed outlier: 6.502A pdb=" N VAL 4 75 " --> pdb=" O LEU 4 86 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ALA 4 74 " --> pdb=" O SER 4 24 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU 4 26 " --> pdb=" O ALA 4 74 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE 4 76 " --> pdb=" O LEU 4 26 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL 4 28 " --> pdb=" O ILE 4 76 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ALA 4 78 " --> pdb=" O VAL 4 28 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE 4 30 " --> pdb=" O ALA 4 78 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS 4 173 " --> pdb=" O LEU 4 25 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N THR 4 27 " --> pdb=" O LYS 4 173 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG 4 175 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE 4 29 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU 4 177 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLU 4 31 " --> pdb=" O LEU 4 177 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU 4 179 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL 4 178 " --> pdb=" O PRO 4 209 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP 4 211 " --> pdb=" O VAL 4 178 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N THR 4 180 " --> pdb=" O ASP 4 211 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL 4 213 " --> pdb=" O THR 4 180 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '5' and resid 8 through 11 Processing sheet with id= M, first strand: chain '6' and resid 178 through 183 removed outlier: 6.168A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N THR 6 229 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE 6 127 " --> pdb=" O THR 6 229 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU 6 231 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N THR 6 129 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU 6 233 " --> pdb=" O THR 6 129 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ASP 6 131 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL 6 235 " --> pdb=" O ASP 6 131 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG 6 260 " --> pdb=" O VAL 6 232 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE 6 234 " --> pdb=" O ARG 6 260 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS 6 262 " --> pdb=" O ILE 6 234 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '6' and resid 427 through 429 removed outlier: 3.702A pdb=" N GLN 6 434 " --> pdb=" O CYS 6 429 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '7' and resid 132 through 134 removed outlier: 6.473A pdb=" N LYS 7 174 " --> pdb=" O PRO 7 163 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '7' and resid 224 through 228 removed outlier: 4.476A pdb=" N TYR 7 232 " --> pdb=" O ILE 7 318 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE 7 316 " --> pdb=" O VAL 7 234 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '7' and resid 435 through 438 removed outlier: 6.305A pdb=" N LEU 7 452 " --> pdb=" O ALA 7 436 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE 7 438 " --> pdb=" O LEU 7 452 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL 7 454 " --> pdb=" O PHE 7 438 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL 7 407 " --> pdb=" O VAL 7 453 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N SER 7 455 " --> pdb=" O VAL 7 407 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL 7 409 " --> pdb=" O SER 7 455 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE 7 484 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU 7 410 " --> pdb=" O PHE 7 484 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE 7 486 " --> pdb=" O LEU 7 410 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY 7 382 " --> pdb=" O GLY 7 512 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR 7 514 " --> pdb=" O GLY 7 382 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE 7 384 " --> pdb=" O THR 7 514 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N VAL 7 385 " --> pdb=" O PRO 7 533 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N LEU 7 535 " --> pdb=" O VAL 7 385 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '7' and resid 552 through 554 removed outlier: 7.160A pdb=" N ALA 7 703 " --> pdb=" O GLN 7 553 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '7' and resid 734 through 736 Processing sheet with id= T, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= U, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= V, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.611A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.510A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.265A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.204A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 588 through 590 removed outlier: 3.669A pdb=" N PHE A 614 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 879 through 882 Processing sheet with id= AB, first strand: chain 'A' and resid 1115 through 1119 removed outlier: 3.566A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.214A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A1149 " --> pdb=" O GLU A1196 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 69 through 73 Processing sheet with id= AE, first strand: chain 'B' and resid 95 through 97 Processing sheet with id= AF, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= AG, first strand: chain 'B' and resid 125 through 127 Processing sheet with id= AH, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= AI, first strand: chain 'B' and resid 404 through 407 Processing sheet with id= AJ, first strand: chain 'B' and resid 224 through 227 removed outlier: 6.882A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ARG B 241 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N SER B 252 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'B' and resid 543 through 545 Processing sheet with id= AL, first strand: chain 'B' and resid 614 through 618 removed outlier: 6.428A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 792 through 796 removed outlier: 5.749A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'B' and resid 1086 through 1092 removed outlier: 4.334A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B1010 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N MET B 839 " --> pdb=" O LYS B 987 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR B 989 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N MET B 841 " --> pdb=" O THR B 989 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY B 991 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'B' and resid 872 through 874 Processing sheet with id= AP, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id= AQ, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id= AR, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.644A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'C' and resid 97 through 104 removed outlier: 6.092A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'C' and resid 111 through 114 Processing sheet with id= AU, first strand: chain 'D' and resid 36 through 38 Processing sheet with id= AV, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.741A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'E' and resid 152 through 155 Processing sheet with id= AX, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AY, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.288A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'G' and resid 142 through 146 removed outlier: 6.822A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ILE G 157 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N PHE G 109 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA G 159 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'G' and resid 120 through 122 Processing sheet with id= BB, first strand: chain 'H' and resid 23 through 29 removed outlier: 5.472A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'I' and resid 14 through 19 Processing sheet with id= BD, first strand: chain 'I' and resid 69 through 71 removed outlier: 3.974A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.743A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'L' and resid 37 through 40 Processing sheet with id= BG, first strand: chain 'M' and resid 34 through 37 removed outlier: 6.417A pdb=" N CYS M 45 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL M 51 " --> pdb=" O CYS M 45 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'O' and resid 155 through 157 removed outlier: 4.201A pdb=" N LYS O 120 " --> pdb=" O PHE O 116 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR O 111 " --> pdb=" O ILE O 106 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'O' and resid 193 through 197 removed outlier: 3.515A pdb=" N GLY O 216 " --> pdb=" O ILE O 160 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE O 160 " --> pdb=" O GLY O 216 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER O 163 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU O 67 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'Q' and resid 103 through 105 removed outlier: 6.319A pdb=" N PHE Q 384 " --> pdb=" O ARG Q 104 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'Q' and resid 117 through 122 removed outlier: 6.604A pdb=" N LYS Q 391 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LYS Q 120 " --> pdb=" O LYS Q 391 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR Q 393 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLN Q 122 " --> pdb=" O TYR Q 393 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE Q 395 " --> pdb=" O GLN Q 122 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL Q 392 " --> pdb=" O GLU Q 366 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'R' and resid 93 through 97 removed outlier: 4.428A pdb=" N ILE R 104 " --> pdb=" O LEU R 122 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU R 221 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU R 70 " --> pdb=" O CYS R 219 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU R 221 " --> pdb=" O LEU R 70 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ARG R 72 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLN R 223 " --> pdb=" O ARG R 72 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'R' and resid 135 through 138 removed outlier: 3.878A pdb=" N ALA R 213 " --> pdb=" O THR R 136 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'R' and resid 337 through 340 removed outlier: 3.617A pdb=" N VAL R 340 " --> pdb=" O LYS R 348 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS R 348 " --> pdb=" O VAL R 340 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'U' and resid 243 through 245 Processing sheet with id= BP, first strand: chain 'U' and resid 278 through 284 removed outlier: 6.352A pdb=" N LYS U 263 " --> pdb=" O TYR U 248 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR U 248 " --> pdb=" O LYS U 263 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'V' and resid 60 through 63 Processing sheet with id= BR, first strand: chain 'V' and resid 110 through 116 removed outlier: 3.708A pdb=" N THR V 68 " --> pdb=" O ILE V 79 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS V 81 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU V 66 " --> pdb=" O LYS V 81 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'W' and resid 68 through 74 Processing sheet with id= BT, first strand: chain 'X' and resid 169 through 172 Processing sheet with id= BU, first strand: chain 'X' and resid 230 through 232 2617 hydrogen bonds defined for protein. 7233 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: 29.77 Time building geometry restraints manager: 23.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 29770 1.42 - 1.63: 44094 1.63 - 1.85: 628 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 74504 Sorted by residual: bond pdb=" C4 ADP 7 903 " pdb=" C5 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" BE BEF 7 901 " pdb=" F2 BEF 7 901 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C5 ADP 7 903 " pdb=" C6 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" CA LYS 0 499 " pdb=" C LYS 0 499 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.24e-02 6.50e+03 1.37e+01 bond pdb=" BE BEF 7 901 " pdb=" F3 BEF 7 901 " ideal model delta sigma weight residual 1.476 1.544 -0.068 2.00e-02 2.50e+03 1.14e+01 ... (remaining 74499 not shown) Histogram of bond angle deviations from ideal: 73.65 - 85.82: 12 85.82 - 97.98: 0 97.98 - 110.15: 14350 110.15 - 122.31: 75126 122.31 - 134.48: 11447 Bond angle restraints: 100935 Sorted by residual: angle pdb=" N TYR 7 677 " pdb=" CA TYR 7 677 " pdb=" C TYR 7 677 " ideal model delta sigma weight residual 108.31 116.51 -8.20 1.52e+00 4.33e-01 2.91e+01 angle pdb=" C GLN A 525 " pdb=" CA GLN A 525 " pdb=" CB GLN A 525 " ideal model delta sigma weight residual 117.23 110.00 7.23 1.36e+00 5.41e-01 2.83e+01 angle pdb=" CA GLN A 525 " pdb=" C GLN A 525 " pdb=" N ASP A 526 " ideal model delta sigma weight residual 119.98 115.58 4.40 8.50e-01 1.38e+00 2.68e+01 angle pdb=" N GLN A 525 " pdb=" CA GLN A 525 " pdb=" C GLN A 525 " ideal model delta sigma weight residual 108.67 117.03 -8.36 1.67e+00 3.59e-01 2.50e+01 angle pdb=" C ALA A 506 " pdb=" N VAL A 507 " pdb=" CA VAL A 507 " ideal model delta sigma weight residual 120.24 123.03 -2.79 6.30e-01 2.52e+00 1.97e+01 ... (remaining 100930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 44457 34.94 - 69.88: 998 69.88 - 104.83: 103 104.83 - 139.77: 2 139.77 - 174.71: 1 Dihedral angle restraints: 45561 sinusoidal: 19551 harmonic: 26010 Sorted by residual: dihedral pdb=" O2A ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" PB ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 71.03 -131.02 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" C5' ADP 7 903 " pdb=" O5' ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" O2A ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 -172.27 112.27 1 2.00e+01 2.50e-03 3.31e+01 dihedral pdb=" C TYR A 465 " pdb=" N TYR A 465 " pdb=" CA TYR A 465 " pdb=" CB TYR A 465 " ideal model delta harmonic sigma weight residual -122.60 -135.98 13.38 0 2.50e+00 1.60e-01 2.87e+01 ... (remaining 45558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 10966 0.101 - 0.202: 438 0.202 - 0.303: 3 0.303 - 0.404: 0 0.404 - 0.504: 1 Chirality restraints: 11408 Sorted by residual: chirality pdb=" CA TYR A 465 " pdb=" N TYR A 465 " pdb=" C TYR A 465 " pdb=" CB TYR A 465 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.36e+00 chirality pdb=" CA GLN A 525 " pdb=" N GLN A 525 " pdb=" C GLN A 525 " pdb=" CB GLN A 525 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C3' ADP 7 903 " pdb=" C2' ADP 7 903 " pdb=" C4' ADP 7 903 " pdb=" O3' ADP 7 903 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 11405 not shown) Planarity restraints: 12645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 975 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" CD GLN B 975 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLN B 975 " 0.017 2.00e-02 2.50e+03 pdb=" NE2 GLN B 975 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO W 208 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO W 209 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO W 209 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO W 209 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU O 108 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO O 109 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO O 109 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO O 109 " -0.034 5.00e-02 4.00e+02 ... (remaining 12642 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 298 2.51 - 3.11: 53593 3.11 - 3.70: 109591 3.70 - 4.30: 164885 4.30 - 4.90: 269100 Nonbonded interactions: 597467 Sorted by model distance: nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 1.910 2.170 nonbonded pdb=" OD1 ASP B 326 " pdb=" OG1 THR B 329 " model vdw 1.922 2.440 nonbonded pdb=" O HIS O 179 " pdb=" OG SER O 183 " model vdw 1.976 2.440 nonbonded pdb=" F1 BEF 7 901 " pdb="MG MG 7 902 " model vdw 2.000 2.120 nonbonded pdb="MG MG 7 902 " pdb=" O1B ADP 7 903 " model vdw 2.001 2.170 ... (remaining 597462 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.450 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: 0.070 Extract box with map and model: 13.510 Check model and map are aligned: 0.800 Set scattering table: 0.520 Process input model: 168.500 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 203.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.003 0.109 74504 Z= 0.172 Angle : 0.499 12.480 100935 Z= 0.291 Chirality : 0.040 0.504 11408 Planarity : 0.003 0.065 12645 Dihedral : 14.787 174.712 28667 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.01 % Allowed : 0.30 % Favored : 99.69 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.31 (0.09), residues: 8759 helix: 1.11 (0.09), residues: 3516 sheet: -0.26 (0.14), residues: 1273 loop : -0.36 (0.10), residues: 3970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 313 HIS 0.006 0.001 HIS W 93 PHE 0.024 0.001 PHE A 252 TYR 0.017 0.001 TYR A 465 ARG 0.010 0.000 ARG 7 680 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1754 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1753 time to evaluate : 6.178 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: symmetry clash REVERT: 0 90 MET cc_start: 0.9008 (mmm) cc_final: 0.8669 (mmm) REVERT: 0 183 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8078 (tppp) REVERT: 0 210 TYR cc_start: 0.8706 (m-80) cc_final: 0.7879 (m-80) REVERT: 0 327 ARG cc_start: 0.7304 (mmt180) cc_final: 0.6976 (mmt90) REVERT: 0 352 ILE cc_start: 0.8841 (mt) cc_final: 0.8640 (mm) REVERT: 0 427 ASN cc_start: 0.7574 (t0) cc_final: 0.7374 (t0) REVERT: 0 581 LEU cc_start: 0.8855 (mp) cc_final: 0.8527 (mm) REVERT: 1 87 HIS cc_start: 0.8339 (m-70) cc_final: 0.7839 (m170) REVERT: 1 315 LEU cc_start: 0.8643 (mt) cc_final: 0.8380 (mp) REVERT: 1 343 ILE cc_start: 0.8597 (pt) cc_final: 0.8309 (mp) REVERT: 1 628 HIS cc_start: 0.8049 (t-90) cc_final: 0.7835 (t-90) REVERT: 1 634 PHE cc_start: 0.8095 (t80) cc_final: 0.7720 (t80) REVERT: 2 411 LEU cc_start: 0.8867 (tp) cc_final: 0.8288 (mm) REVERT: 4 119 ARG cc_start: 0.7621 (ttt-90) cc_final: 0.7415 (ttp80) REVERT: 4 281 ARG cc_start: 0.7200 (ptt-90) cc_final: 0.6935 (ptt90) REVERT: 6 144 ASN cc_start: 0.7559 (p0) cc_final: 0.7353 (p0) REVERT: 6 199 ILE cc_start: 0.8225 (mt) cc_final: 0.8007 (mp) REVERT: 6 398 PHE cc_start: 0.7906 (m-80) cc_final: 0.7522 (m-10) REVERT: 7 174 LYS cc_start: 0.8566 (tttt) cc_final: 0.8002 (ttmm) REVERT: 7 497 MET cc_start: 0.7975 (tpp) cc_final: 0.7574 (tpp) REVERT: 7 546 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8267 (mttt) REVERT: 7 644 GLN cc_start: 0.7900 (mt0) cc_final: 0.7633 (mt0) REVERT: 7 674 SER cc_start: 0.9004 (t) cc_final: 0.8762 (m) REVERT: 7 694 LYS cc_start: 0.8717 (tmtt) cc_final: 0.8472 (tmtm) REVERT: A 163 SER cc_start: 0.8840 (m) cc_final: 0.8223 (m) REVERT: A 609 ASP cc_start: 0.7589 (t70) cc_final: 0.7104 (t0) REVERT: A 620 LYS cc_start: 0.8424 (mttm) cc_final: 0.8223 (mtmm) REVERT: A 895 LYS cc_start: 0.8417 (tptm) cc_final: 0.8146 (tptp) REVERT: A 926 GLN cc_start: 0.7982 (tp40) cc_final: 0.7758 (tp-100) REVERT: A 945 GLU cc_start: 0.7484 (tt0) cc_final: 0.7229 (tt0) REVERT: A 965 GLN cc_start: 0.8240 (mt0) cc_final: 0.8031 (mt0) REVERT: A 1009 ASN cc_start: 0.8660 (m-40) cc_final: 0.8447 (m-40) REVERT: B 312 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7609 (tm-30) REVERT: B 315 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8414 (mtpp) REVERT: B 320 ASP cc_start: 0.8029 (t0) cc_final: 0.7757 (t0) REVERT: B 325 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8253 (mm110) REVERT: B 332 ASP cc_start: 0.7516 (t0) cc_final: 0.7122 (t0) REVERT: B 336 ARG cc_start: 0.8215 (ptp-170) cc_final: 0.7923 (ptp90) REVERT: B 358 LYS cc_start: 0.8405 (mtmt) cc_final: 0.8120 (mtmt) REVERT: B 763 GLN cc_start: 0.8105 (tt0) cc_final: 0.7759 (tt0) REVERT: D 61 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7483 (tm-30) REVERT: D 157 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7999 (mm-40) REVERT: E 50 MET cc_start: 0.6403 (ttp) cc_final: 0.5868 (tmm) REVERT: G 167 TYR cc_start: 0.8703 (m-80) cc_final: 0.8476 (m-80) REVERT: H 9 ILE cc_start: 0.8716 (mt) cc_final: 0.8489 (mt) REVERT: H 11 GLN cc_start: 0.8372 (tt0) cc_final: 0.8154 (tt0) REVERT: H 37 LYS cc_start: 0.8704 (pttt) cc_final: 0.8444 (ptmm) REVERT: H 131 ASN cc_start: 0.8213 (m-40) cc_final: 0.7820 (m-40) REVERT: I 97 MET cc_start: 0.8749 (mtp) cc_final: 0.8405 (mtm) REVERT: K 54 ARG cc_start: 0.7501 (mmm160) cc_final: 0.7250 (mmm160) REVERT: K 55 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8442 (mtpt) REVERT: K 102 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8274 (ttmt) REVERT: M 149 CYS cc_start: 0.8352 (m) cc_final: 0.8014 (m) REVERT: M 193 GLN cc_start: 0.8671 (mt0) cc_final: 0.8364 (tt0) REVERT: M 277 ILE cc_start: 0.8457 (mt) cc_final: 0.8166 (mm) REVERT: M 305 THR cc_start: 0.8481 (m) cc_final: 0.8177 (p) REVERT: M 337 ASP cc_start: 0.7000 (t0) cc_final: 0.6670 (t0) REVERT: Q 359 ASN cc_start: 0.8779 (m-40) cc_final: 0.8569 (m110) REVERT: Q 373 TYR cc_start: 0.7898 (m-10) cc_final: 0.7668 (m-10) REVERT: R 208 ILE cc_start: 0.9199 (mt) cc_final: 0.8972 (tt) REVERT: R 323 ARG cc_start: 0.7636 (mtp180) cc_final: 0.7261 (tmm160) REVERT: W 135 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7577 (mt-10) REVERT: X 218 ASP cc_start: 0.7309 (m-30) cc_final: 0.6988 (m-30) REVERT: X 222 ASN cc_start: 0.8962 (m-40) cc_final: 0.8752 (m110) outliers start: 1 outliers final: 6 residues processed: 1754 average time/residue: 1.5747 time to fit residues: 3598.0697 Evaluate side-chains 1358 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1352 time to evaluate : 6.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 195 ILE Chi-restraints excluded: chain 2 residue 182 PHE Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain W residue 170 ASP Chi-restraints excluded: chain X residue 221 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 748 optimal weight: 10.0000 chunk 671 optimal weight: 0.9990 chunk 372 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 452 optimal weight: 4.9990 chunk 358 optimal weight: 3.9990 chunk 694 optimal weight: 1.9990 chunk 268 optimal weight: 20.0000 chunk 422 optimal weight: 0.0670 chunk 516 optimal weight: 6.9990 chunk 804 optimal weight: 3.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 113 ASN 0 164 ASN 0 302 GLN 0 324 ASN 1 196 GLN 1 250 ASN 1 467 GLN 1 513 GLN 1 554 HIS 2 395 GLN 3 122 HIS 4 266 ASN 6 114 ASN 6 176 ASN 6 180 GLN 6 207 ASN ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 169 HIS 7 247 ASN ** 7 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 ASN A 969 GLN A1218 GLN B 366 GLN B 449 ASN B 465 ASN B 513 GLN B 531 GLN B 686 ASN B1062 HIS C 224 GLN D 34 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 102 GLN G 131 GLN I 90 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 290 GLN O 69 ASN O 225 GLN Q 117 HIS Q 122 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 178 GLN W 353 ASN X 199 GLN ** X 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 74504 Z= 0.349 Angle : 0.609 12.040 100935 Z= 0.318 Chirality : 0.045 0.212 11408 Planarity : 0.005 0.053 12645 Dihedral : 10.355 177.710 10650 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.43 % Allowed : 10.64 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.19 (0.09), residues: 8759 helix: 0.94 (0.09), residues: 3546 sheet: -0.16 (0.14), residues: 1297 loop : -0.43 (0.10), residues: 3916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 954 HIS 0.010 0.001 HIS W 93 PHE 0.035 0.002 PHE W 228 TYR 0.028 0.002 TYR M 317 ARG 0.010 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1567 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1374 time to evaluate : 6.254 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: symmetry clash revert: symmetry clash REVERT: 0 90 MET cc_start: 0.9058 (mmm) cc_final: 0.8735 (mmm) REVERT: 0 183 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7997 (tppp) REVERT: 0 269 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6947 (tp30) REVERT: 0 327 ARG cc_start: 0.7329 (mmt180) cc_final: 0.6991 (mmt90) REVERT: 0 352 ILE cc_start: 0.8819 (mt) cc_final: 0.8594 (mm) REVERT: 0 379 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7689 (tp30) REVERT: 0 581 LEU cc_start: 0.8841 (mp) cc_final: 0.8498 (mm) REVERT: 1 87 HIS cc_start: 0.8584 (m-70) cc_final: 0.8141 (m-70) REVERT: 1 628 HIS cc_start: 0.8051 (t-90) cc_final: 0.7846 (t-90) REVERT: 1 634 PHE cc_start: 0.8203 (t80) cc_final: 0.7831 (t80) REVERT: 2 198 SER cc_start: 0.8682 (t) cc_final: 0.8444 (m) REVERT: 2 261 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6429 (tt0) REVERT: 2 416 LEU cc_start: 0.9070 (tt) cc_final: 0.8803 (tm) REVERT: 4 119 ARG cc_start: 0.7683 (ttt-90) cc_final: 0.7463 (ttp80) REVERT: 6 134 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6992 (mm-30) REVERT: 6 152 TYR cc_start: 0.8632 (m-80) cc_final: 0.8182 (m-80) REVERT: 6 342 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7959 (mt) REVERT: 6 398 PHE cc_start: 0.8018 (m-80) cc_final: 0.7533 (m-10) REVERT: 6 409 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7582 (tpp80) REVERT: 7 154 GLN cc_start: 0.7926 (mt0) cc_final: 0.7698 (mt0) REVERT: 7 174 LYS cc_start: 0.8474 (tttt) cc_final: 0.7808 (ttmm) REVERT: 7 546 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8262 (mttm) REVERT: 7 600 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7842 (tpp80) REVERT: 7 694 LYS cc_start: 0.8784 (tmtt) cc_final: 0.8485 (tmtm) REVERT: 7 832 LEU cc_start: 0.8727 (tp) cc_final: 0.8385 (tt) REVERT: A 41 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7525 (mtt) REVERT: A 260 ASP cc_start: 0.7814 (t70) cc_final: 0.7420 (t70) REVERT: A 414 ASP cc_start: 0.7585 (t0) cc_final: 0.7212 (t70) REVERT: A 486 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7725 (mt-10) REVERT: A 609 ASP cc_start: 0.7541 (t70) cc_final: 0.7147 (t0) REVERT: A 620 LYS cc_start: 0.8478 (mttm) cc_final: 0.8246 (mtmm) REVERT: A 773 LYS cc_start: 0.7833 (tptp) cc_final: 0.7603 (tptt) REVERT: A 895 LYS cc_start: 0.8434 (tptm) cc_final: 0.8202 (tptp) REVERT: A 926 GLN cc_start: 0.8391 (tp40) cc_final: 0.8127 (tp-100) REVERT: A 965 GLN cc_start: 0.8257 (mt0) cc_final: 0.8050 (mt0) REVERT: A 1309 ASP cc_start: 0.7845 (m-30) cc_final: 0.7578 (m-30) REVERT: A 1444 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8195 (mmm) REVERT: B 65 GLU cc_start: 0.6822 (mm-30) cc_final: 0.6604 (mm-30) REVERT: B 151 LEU cc_start: 0.8550 (tt) cc_final: 0.8310 (tt) REVERT: B 312 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7566 (tm-30) REVERT: B 315 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8400 (mtpp) REVERT: B 320 ASP cc_start: 0.8012 (t0) cc_final: 0.7692 (t0) REVERT: B 332 ASP cc_start: 0.7507 (t0) cc_final: 0.7179 (t0) REVERT: B 336 ARG cc_start: 0.8391 (ptp-170) cc_final: 0.8162 (ptp-170) REVERT: B 353 LYS cc_start: 0.8550 (ttmt) cc_final: 0.8240 (mtpm) REVERT: B 358 LYS cc_start: 0.8541 (mtmt) cc_final: 0.8058 (mtmt) REVERT: B 392 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7552 (mtt-85) REVERT: B 426 LYS cc_start: 0.8050 (mmtp) cc_final: 0.7800 (mmpt) REVERT: B 560 GLU cc_start: 0.7269 (mm-30) cc_final: 0.7045 (mm-30) REVERT: B 763 GLN cc_start: 0.8053 (tt0) cc_final: 0.7734 (tt0) REVERT: B 969 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8734 (ttp-110) REVERT: C 79 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7984 (mt0) REVERT: D 61 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7490 (tm-30) REVERT: D 155 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6524 (tpt-90) REVERT: D 157 GLN cc_start: 0.8283 (mm-40) cc_final: 0.8010 (mm-40) REVERT: E 162 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7556 (ttp80) REVERT: G 1 MET cc_start: 0.8202 (tpp) cc_final: 0.7725 (tpt) REVERT: G 33 GLU cc_start: 0.7156 (tt0) cc_final: 0.6876 (tt0) REVERT: G 100 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7838 (mt-10) REVERT: G 167 TYR cc_start: 0.8703 (m-80) cc_final: 0.8439 (m-80) REVERT: H 37 LYS cc_start: 0.8572 (pttt) cc_final: 0.8362 (ptmt) REVERT: I 97 MET cc_start: 0.8792 (mtp) cc_final: 0.8429 (mtm) REVERT: K 54 ARG cc_start: 0.7520 (mmm160) cc_final: 0.7259 (mmm160) REVERT: K 55 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8498 (mtpt) REVERT: K 102 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8278 (ttmt) REVERT: M 33 LYS cc_start: 0.7389 (mmtm) cc_final: 0.7146 (mtpp) REVERT: M 145 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8411 (tt) REVERT: M 149 CYS cc_start: 0.8360 (m) cc_final: 0.8014 (m) REVERT: M 193 GLN cc_start: 0.8766 (mt0) cc_final: 0.8444 (tt0) REVERT: M 337 ASP cc_start: 0.7065 (t0) cc_final: 0.6746 (t0) REVERT: Q 34 MET cc_start: 0.4736 (ttm) cc_final: 0.3781 (ttm) REVERT: Q 364 SER cc_start: 0.8302 (t) cc_final: 0.7898 (m) REVERT: Q 373 TYR cc_start: 0.7833 (m-10) cc_final: 0.7621 (m-10) REVERT: R 270 MET cc_start: 0.8371 (mmm) cc_final: 0.7588 (mmm) REVERT: R 349 TYR cc_start: 0.7214 (m-80) cc_final: 0.7009 (m-80) REVERT: W 50 ASN cc_start: 0.7563 (OUTLIER) cc_final: 0.7361 (p0) REVERT: W 135 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7585 (mt-10) REVERT: W 170 ASP cc_start: 0.8015 (t70) cc_final: 0.7693 (t0) REVERT: X 225 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6826 (tt0) REVERT: X 261 LYS cc_start: 0.8192 (tppt) cc_final: 0.7832 (mmmm) outliers start: 193 outliers final: 69 residues processed: 1451 average time/residue: 1.6020 time to fit residues: 3021.8857 Evaluate side-chains 1373 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1291 time to evaluate : 6.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 76 MET Chi-restraints excluded: chain 0 residue 295 SER Chi-restraints excluded: chain 0 residue 309 THR Chi-restraints excluded: chain 0 residue 379 GLU Chi-restraints excluded: chain 0 residue 455 SER Chi-restraints excluded: chain 0 residue 467 ASP Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 625 ILE Chi-restraints excluded: chain 0 residue 709 SER Chi-restraints excluded: chain 1 residue 175 LEU Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 436 HIS Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 2 residue 182 PHE Chi-restraints excluded: chain 2 residue 261 GLN Chi-restraints excluded: chain 2 residue 448 LEU Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 266 ASN Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 342 LEU Chi-restraints excluded: chain 6 residue 409 ARG Chi-restraints excluded: chain 7 residue 226 VAL Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 675 SER Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 880 LYS Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 1392 SER Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 969 ARG Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain M residue 145 ILE Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 130 ASP Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 136 SER Chi-restraints excluded: chain O residue 172 LEU Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain X residue 225 GLU Chi-restraints excluded: chain X residue 228 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 447 optimal weight: 0.9980 chunk 249 optimal weight: 0.8980 chunk 669 optimal weight: 6.9990 chunk 547 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 806 optimal weight: 1.9990 chunk 870 optimal weight: 9.9990 chunk 717 optimal weight: 0.9990 chunk 799 optimal weight: 4.9990 chunk 274 optimal weight: 0.5980 chunk 646 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 164 ASN 1 49 GLN 3 90 ASN 4 266 ASN ** 4 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 176 ASN 7 685 GLN A 45 GLN A 119 ASN A 425 GLN A 471 ASN A 517 ASN A 700 ASN A 969 GLN A1009 ASN B 366 GLN B 449 ASN B 686 ASN B 887 HIS D 34 GLN D 37 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 131 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN I 90 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 GLN X 199 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 74504 Z= 0.214 Angle : 0.529 11.447 100935 Z= 0.277 Chirality : 0.042 0.163 11408 Planarity : 0.004 0.058 12645 Dihedral : 10.256 179.098 10642 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.39 % Allowed : 13.11 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.27 (0.09), residues: 8759 helix: 1.04 (0.09), residues: 3547 sheet: -0.10 (0.14), residues: 1314 loop : -0.42 (0.10), residues: 3898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 954 HIS 0.005 0.001 HIS A 659 PHE 0.030 0.001 PHE W 228 TYR 0.030 0.001 TYR M 317 ARG 0.008 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1512 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1322 time to evaluate : 6.203 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 90 MET cc_start: 0.9090 (mmm) cc_final: 0.8671 (mmm) REVERT: 0 183 LYS cc_start: 0.8306 (ttmt) cc_final: 0.8008 (tppp) REVERT: 0 269 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6886 (tp30) REVERT: 0 281 LYS cc_start: 0.8408 (mtpm) cc_final: 0.8078 (mtpt) REVERT: 0 327 ARG cc_start: 0.7352 (mmt180) cc_final: 0.7035 (mmt90) REVERT: 0 352 ILE cc_start: 0.8778 (mt) cc_final: 0.8537 (mm) REVERT: 0 427 ASN cc_start: 0.7632 (t0) cc_final: 0.7388 (t0) REVERT: 0 581 LEU cc_start: 0.8820 (mp) cc_final: 0.8473 (mm) REVERT: 1 59 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7412 (mmt) REVERT: 1 87 HIS cc_start: 0.8566 (m-70) cc_final: 0.8114 (m-70) REVERT: 1 634 PHE cc_start: 0.8167 (t80) cc_final: 0.7794 (t80) REVERT: 2 198 SER cc_start: 0.8620 (t) cc_final: 0.8409 (m) REVERT: 2 227 MET cc_start: 0.8171 (tmm) cc_final: 0.7903 (tmm) REVERT: 2 416 LEU cc_start: 0.9091 (tt) cc_final: 0.8838 (tm) REVERT: 3 40 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: 4 119 ARG cc_start: 0.7704 (ttt-90) cc_final: 0.7494 (ttp80) REVERT: 6 398 PHE cc_start: 0.8006 (m-80) cc_final: 0.7569 (m-10) REVERT: 7 174 LYS cc_start: 0.8428 (tttt) cc_final: 0.7785 (ttmm) REVERT: 7 546 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8344 (mttp) REVERT: 7 694 LYS cc_start: 0.8829 (tmtt) cc_final: 0.8503 (tmtm) REVERT: 7 832 LEU cc_start: 0.8705 (tp) cc_final: 0.8351 (tt) REVERT: A 4 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: A 120 GLU cc_start: 0.6833 (mp0) cc_final: 0.6563 (mp0) REVERT: A 124 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7627 (mp-120) REVERT: A 260 ASP cc_start: 0.7869 (t70) cc_final: 0.7400 (t70) REVERT: A 427 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: A 486 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7730 (mt-10) REVERT: A 609 ASP cc_start: 0.7564 (t70) cc_final: 0.7177 (t0) REVERT: A 806 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7810 (mtt-85) REVERT: A 822 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7084 (tt0) REVERT: A 895 LYS cc_start: 0.8392 (tptm) cc_final: 0.8174 (tptp) REVERT: A 926 GLN cc_start: 0.8308 (tp40) cc_final: 0.8106 (tp-100) REVERT: A 965 GLN cc_start: 0.8225 (mt0) cc_final: 0.7986 (mt0) REVERT: A 1309 ASP cc_start: 0.7996 (m-30) cc_final: 0.7751 (m-30) REVERT: A 1315 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7211 (mt-10) REVERT: A 1337 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7357 (mm-30) REVERT: B 312 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7475 (tm-30) REVERT: B 315 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8348 (mtpp) REVERT: B 320 ASP cc_start: 0.8048 (t70) cc_final: 0.7741 (t0) REVERT: B 332 ASP cc_start: 0.7546 (t0) cc_final: 0.7174 (t0) REVERT: B 336 ARG cc_start: 0.8394 (ptp-170) cc_final: 0.8064 (ptp-110) REVERT: B 358 LYS cc_start: 0.8502 (mtmt) cc_final: 0.8106 (mtmt) REVERT: B 484 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.7878 (m-40) REVERT: B 560 GLU cc_start: 0.7255 (mm-30) cc_final: 0.7023 (mm-30) REVERT: B 620 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7993 (mpp80) REVERT: C 26 ASP cc_start: 0.7148 (p0) cc_final: 0.6908 (p0) REVERT: C 79 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7967 (mt0) REVERT: D 61 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7456 (tm-30) REVERT: D 157 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7996 (mm-40) REVERT: G 1 MET cc_start: 0.8189 (tpp) cc_final: 0.7670 (tpt) REVERT: G 33 GLU cc_start: 0.7181 (tt0) cc_final: 0.6864 (tt0) REVERT: G 167 TYR cc_start: 0.8692 (m-80) cc_final: 0.8437 (m-80) REVERT: H 37 LYS cc_start: 0.8605 (pttt) cc_final: 0.8371 (ptmt) REVERT: I 97 MET cc_start: 0.8769 (mtp) cc_final: 0.8420 (mtm) REVERT: K 54 ARG cc_start: 0.7508 (mmm160) cc_final: 0.7237 (mmm160) REVERT: K 55 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8470 (mtpt) REVERT: K 102 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8191 (ttmt) REVERT: M 145 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8403 (tt) REVERT: M 193 GLN cc_start: 0.8758 (mt0) cc_final: 0.8476 (tt0) REVERT: M 287 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8458 (mt) REVERT: O 171 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7995 (ttp80) REVERT: Q 34 MET cc_start: 0.4769 (ttm) cc_final: 0.3873 (ttm) REVERT: Q 364 SER cc_start: 0.8306 (t) cc_final: 0.7961 (m) REVERT: R 270 MET cc_start: 0.8286 (mmm) cc_final: 0.7686 (mmm) REVERT: R 349 TYR cc_start: 0.7182 (m-80) cc_final: 0.6762 (m-80) REVERT: W 71 LYS cc_start: 0.8545 (mttt) cc_final: 0.8341 (mttp) REVERT: W 135 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7603 (mt-10) REVERT: W 144 ARG cc_start: 0.8289 (mmm160) cc_final: 0.7861 (mmm160) REVERT: W 174 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7800 (mtp85) REVERT: X 225 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6698 (tt0) REVERT: X 261 LYS cc_start: 0.8156 (tppt) cc_final: 0.7793 (mmmm) REVERT: X 320 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8437 (mp) outliers start: 190 outliers final: 75 residues processed: 1397 average time/residue: 1.5829 time to fit residues: 2881.3755 Evaluate side-chains 1353 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1262 time to evaluate : 6.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 76 MET Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 309 THR Chi-restraints excluded: chain 0 residue 467 ASP Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 625 ILE Chi-restraints excluded: chain 0 residue 709 SER Chi-restraints excluded: chain 1 residue 59 MET Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 436 HIS Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 2 residue 182 PHE Chi-restraints excluded: chain 2 residue 448 LEU Chi-restraints excluded: chain 3 residue 40 GLU Chi-restraints excluded: chain 4 residue 111 ASN Chi-restraints excluded: chain 4 residue 125 LEU Chi-restraints excluded: chain 4 residue 138 LYS Chi-restraints excluded: chain 4 residue 204 THR Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 7 residue 226 VAL Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 702 ASN Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 806 ARG Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1315 GLU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 145 ILE Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 136 SER Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 171 ARG Chi-restraints excluded: chain O residue 172 LEU Chi-restraints excluded: chain O residue 184 SER Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 353 GLU Chi-restraints excluded: chain Q residue 413 MET Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 80 LYS Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain X residue 225 GLU Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain X residue 320 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 796 optimal weight: 6.9990 chunk 606 optimal weight: 4.9990 chunk 418 optimal weight: 2.9990 chunk 89 optimal weight: 0.0470 chunk 384 optimal weight: 9.9990 chunk 541 optimal weight: 2.9990 chunk 808 optimal weight: 20.0000 chunk 856 optimal weight: 30.0000 chunk 422 optimal weight: 6.9990 chunk 766 optimal weight: 6.9990 chunk 230 optimal weight: 7.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 164 ASN 1 49 GLN 1 365 ASN 6 407 GLN 7 747 ASN A 64 ASN A 425 GLN A 700 ASN A 742 ASN A 760 GLN A 969 GLN B 366 GLN B 449 ASN B 513 GLN B 686 ASN D 34 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN I 90 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 290 GLN O 225 GLN Q 122 GLN ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 HIS ** R 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 178 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 74504 Z= 0.519 Angle : 0.644 13.273 100935 Z= 0.334 Chirality : 0.048 0.267 11408 Planarity : 0.005 0.075 12645 Dihedral : 10.410 177.880 10642 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.13 % Allowed : 14.29 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.05 (0.09), residues: 8759 helix: 0.78 (0.09), residues: 3567 sheet: -0.14 (0.14), residues: 1315 loop : -0.51 (0.10), residues: 3877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 954 HIS 0.009 0.001 HIS A 659 PHE 0.036 0.002 PHE A 219 TYR 0.028 0.002 TYR B1092 ARG 0.017 0.001 ARG B1106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1556 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1307 time to evaluate : 6.199 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 90 MET cc_start: 0.9080 (mmm) cc_final: 0.8754 (mmm) REVERT: 0 138 ASN cc_start: 0.7879 (t160) cc_final: 0.7611 (t0) REVERT: 0 183 LYS cc_start: 0.8306 (ttmt) cc_final: 0.8022 (tppp) REVERT: 0 269 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6918 (tp30) REVERT: 0 327 ARG cc_start: 0.7466 (mmt180) cc_final: 0.7115 (mmt90) REVERT: 0 352 ILE cc_start: 0.8717 (mt) cc_final: 0.8501 (mm) REVERT: 0 379 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7668 (tp30) REVERT: 0 419 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8925 (mm) REVERT: 0 468 MET cc_start: 0.8948 (ttt) cc_final: 0.8571 (ttt) REVERT: 0 581 LEU cc_start: 0.8845 (mp) cc_final: 0.8490 (mm) REVERT: 0 660 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.7470 (ptm160) REVERT: 1 87 HIS cc_start: 0.8658 (m-70) cc_final: 0.8279 (m-70) REVERT: 1 634 PHE cc_start: 0.8200 (t80) cc_final: 0.7809 (t80) REVERT: 2 198 SER cc_start: 0.8668 (t) cc_final: 0.8433 (m) REVERT: 2 227 MET cc_start: 0.8120 (tmm) cc_final: 0.7833 (tmm) REVERT: 2 416 LEU cc_start: 0.9109 (tt) cc_final: 0.8877 (tm) REVERT: 3 40 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: 3 120 LEU cc_start: 0.9001 (tp) cc_final: 0.8699 (tt) REVERT: 6 398 PHE cc_start: 0.8193 (m-80) cc_final: 0.7720 (m-10) REVERT: 6 409 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7468 (tpp80) REVERT: 7 174 LYS cc_start: 0.8488 (tttt) cc_final: 0.7901 (ttmm) REVERT: 7 329 ARG cc_start: 0.8605 (tpm170) cc_final: 0.8068 (tpt-90) REVERT: 7 493 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8609 (t) REVERT: 7 545 GLN cc_start: 0.7945 (pp30) cc_final: 0.7681 (pp30) REVERT: 7 546 LYS cc_start: 0.8571 (mtpt) cc_final: 0.8198 (mttp) REVERT: 7 633 GLN cc_start: 0.7513 (tm-30) cc_final: 0.7231 (tm-30) REVERT: 7 694 LYS cc_start: 0.8873 (tmtt) cc_final: 0.8471 (tmtm) REVERT: 7 832 LEU cc_start: 0.8703 (tp) cc_final: 0.8354 (tt) REVERT: A 4 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: A 260 ASP cc_start: 0.7849 (t70) cc_final: 0.7411 (t70) REVERT: A 414 ASP cc_start: 0.7703 (t0) cc_final: 0.7410 (t70) REVERT: A 486 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7775 (mt-10) REVERT: A 609 ASP cc_start: 0.7578 (t70) cc_final: 0.7255 (t70) REVERT: A 806 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7987 (mtt-85) REVERT: A 822 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7198 (tt0) REVERT: A 926 GLN cc_start: 0.8490 (tp40) cc_final: 0.8213 (tp-100) REVERT: A 939 ASP cc_start: 0.8232 (m-30) cc_final: 0.7945 (m-30) REVERT: A 965 GLN cc_start: 0.8338 (mt0) cc_final: 0.8124 (mt0) REVERT: A 1048 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8249 (m110) REVERT: A 1309 ASP cc_start: 0.7937 (m-30) cc_final: 0.7600 (m-30) REVERT: A 1315 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: B 312 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7590 (tm-30) REVERT: B 315 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8401 (mtpp) REVERT: B 320 ASP cc_start: 0.8132 (t70) cc_final: 0.7817 (t0) REVERT: B 332 ASP cc_start: 0.7667 (t0) cc_final: 0.7221 (t0) REVERT: B 336 ARG cc_start: 0.8504 (ptp-170) cc_final: 0.8083 (ptp-110) REVERT: B 353 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8281 (mtpm) REVERT: B 358 LYS cc_start: 0.8472 (mtmt) cc_final: 0.8223 (mtmt) REVERT: B 392 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7677 (mtt-85) REVERT: B 426 LYS cc_start: 0.8109 (mmtp) cc_final: 0.7857 (mmpt) REVERT: B 484 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8082 (t0) REVERT: B 560 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7072 (mm-30) REVERT: B 563 MET cc_start: 0.9166 (ttp) cc_final: 0.8870 (ttp) REVERT: B 620 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7986 (mpp80) REVERT: B 969 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8560 (ttp-110) REVERT: C 26 ASP cc_start: 0.7182 (p0) cc_final: 0.6909 (p0) REVERT: C 152 GLU cc_start: 0.7464 (tt0) cc_final: 0.7238 (tt0) REVERT: D 61 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7517 (tm-30) REVERT: D 155 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6565 (tpt-90) REVERT: D 157 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7990 (mm-40) REVERT: G 33 GLU cc_start: 0.7293 (tt0) cc_final: 0.6915 (tt0) REVERT: G 100 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7826 (mt-10) REVERT: G 167 TYR cc_start: 0.8758 (m-80) cc_final: 0.8456 (m-80) REVERT: H 37 LYS cc_start: 0.8634 (pttt) cc_final: 0.8409 (ptmt) REVERT: I 92 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7358 (ptp-110) REVERT: I 97 MET cc_start: 0.8783 (mtp) cc_final: 0.8429 (mtm) REVERT: K 54 ARG cc_start: 0.7585 (mmm160) cc_final: 0.7345 (mmm160) REVERT: K 55 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8482 (mtpt) REVERT: K 102 LYS cc_start: 0.8573 (ttpt) cc_final: 0.8245 (ttmt) REVERT: O 121 MET cc_start: 0.7858 (ttp) cc_final: 0.7385 (ttm) REVERT: Q 364 SER cc_start: 0.8470 (t) cc_final: 0.8059 (m) REVERT: W 50 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.7422 (p0) REVERT: W 144 ARG cc_start: 0.8279 (mmm160) cc_final: 0.7979 (mmm-85) REVERT: X 225 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7082 (tt0) REVERT: X 261 LYS cc_start: 0.8226 (tppt) cc_final: 0.7880 (mmmm) REVERT: X 320 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8481 (mp) outliers start: 249 outliers final: 127 residues processed: 1422 average time/residue: 1.5725 time to fit residues: 2919.0008 Evaluate side-chains 1418 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1271 time to evaluate : 6.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 76 MET Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 261 THR Chi-restraints excluded: chain 0 residue 295 SER Chi-restraints excluded: chain 0 residue 309 THR Chi-restraints excluded: chain 0 residue 366 LEU Chi-restraints excluded: chain 0 residue 377 CYS Chi-restraints excluded: chain 0 residue 379 GLU Chi-restraints excluded: chain 0 residue 419 ILE Chi-restraints excluded: chain 0 residue 435 MET Chi-restraints excluded: chain 0 residue 467 ASP Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 625 ILE Chi-restraints excluded: chain 0 residue 660 ARG Chi-restraints excluded: chain 1 residue 49 GLN Chi-restraints excluded: chain 1 residue 175 LEU Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 301 ILE Chi-restraints excluded: chain 1 residue 333 VAL Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 2 residue 120 SER Chi-restraints excluded: chain 2 residue 182 PHE Chi-restraints excluded: chain 2 residue 259 VAL Chi-restraints excluded: chain 3 residue 40 GLU Chi-restraints excluded: chain 3 residue 103 LEU Chi-restraints excluded: chain 4 residue 125 LEU Chi-restraints excluded: chain 4 residue 138 LYS Chi-restraints excluded: chain 4 residue 204 THR Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 6 residue 174 MET Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 332 THR Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain 6 residue 409 ARG Chi-restraints excluded: chain 7 residue 226 VAL Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 493 VAL Chi-restraints excluded: chain 7 residue 675 SER Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 806 ARG Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 880 LYS Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1315 GLU Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 969 ARG Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1112 GLN Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 329 ILE Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 136 SER Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 172 LEU Chi-restraints excluded: chain O residue 184 SER Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 353 GLU Chi-restraints excluded: chain Q residue 375 LEU Chi-restraints excluded: chain Q residue 378 VAL Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 191 ASP Chi-restraints excluded: chain X residue 209 ASP Chi-restraints excluded: chain X residue 225 GLU Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain X residue 320 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 713 optimal weight: 3.9990 chunk 486 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 637 optimal weight: 0.5980 chunk 353 optimal weight: 1.9990 chunk 730 optimal weight: 0.0270 chunk 591 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 437 optimal weight: 5.9990 chunk 768 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 164 ASN 1 493 ASN 2 19 GLN 2 55 ASN 3 90 ASN 4 266 ASN 4 303 ASN 7 685 GLN A 64 ASN A 425 GLN A 700 ASN A 706 HIS A 969 GLN B 366 GLN B 449 ASN B 513 GLN B 686 ASN B 887 HIS D 34 GLN E 32 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN I 90 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 290 GLN O 225 GLN ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 74504 Z= 0.173 Angle : 0.519 11.747 100935 Z= 0.271 Chirality : 0.041 0.159 11408 Planarity : 0.004 0.064 12645 Dihedral : 10.249 178.506 10642 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.44 % Allowed : 16.00 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.33 (0.09), residues: 8759 helix: 1.08 (0.09), residues: 3560 sheet: -0.04 (0.14), residues: 1315 loop : -0.40 (0.10), residues: 3884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 214 HIS 0.005 0.001 HIS B 572 PHE 0.030 0.001 PHE W 228 TYR 0.022 0.001 TYR M 317 ARG 0.014 0.000 ARG 7 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1297 time to evaluate : 6.348 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 90 MET cc_start: 0.9089 (mmm) cc_final: 0.8659 (mmm) REVERT: 0 95 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8296 (tmmm) REVERT: 0 183 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7989 (tppp) REVERT: 0 210 TYR cc_start: 0.8711 (m-80) cc_final: 0.7864 (m-80) REVERT: 0 221 ARG cc_start: 0.7217 (ttp80) cc_final: 0.6577 (ttt180) REVERT: 0 269 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6859 (tp30) REVERT: 0 289 LEU cc_start: 0.9152 (mt) cc_final: 0.8787 (mt) REVERT: 0 327 ARG cc_start: 0.7360 (mmt180) cc_final: 0.7032 (mmt90) REVERT: 0 352 ILE cc_start: 0.8731 (mt) cc_final: 0.8501 (mm) REVERT: 0 581 LEU cc_start: 0.8816 (mp) cc_final: 0.8477 (mm) REVERT: 0 660 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7334 (ptm160) REVERT: 1 87 HIS cc_start: 0.8630 (m-70) cc_final: 0.8294 (m-70) REVERT: 1 192 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7888 (tpt) REVERT: 1 634 PHE cc_start: 0.8193 (t80) cc_final: 0.7797 (t80) REVERT: 2 198 SER cc_start: 0.8630 (t) cc_final: 0.8378 (m) REVERT: 2 227 MET cc_start: 0.8126 (tmm) cc_final: 0.7798 (tmm) REVERT: 2 416 LEU cc_start: 0.9095 (tt) cc_final: 0.8870 (tm) REVERT: 3 120 LEU cc_start: 0.8960 (tp) cc_final: 0.8670 (tt) REVERT: 6 398 PHE cc_start: 0.8106 (m-80) cc_final: 0.7633 (m-10) REVERT: 7 174 LYS cc_start: 0.8497 (tttt) cc_final: 0.7858 (ttmm) REVERT: 7 199 ARG cc_start: 0.7632 (mtm180) cc_final: 0.7417 (mtm180) REVERT: 7 329 ARG cc_start: 0.8583 (tpm170) cc_final: 0.8228 (tpt-90) REVERT: 7 546 LYS cc_start: 0.8545 (mtpt) cc_final: 0.8309 (mttp) REVERT: 7 633 GLN cc_start: 0.7383 (tm-30) cc_final: 0.7083 (tm-30) REVERT: 7 694 LYS cc_start: 0.8839 (tmtt) cc_final: 0.8410 (tmtm) REVERT: 7 832 LEU cc_start: 0.8710 (tp) cc_final: 0.8357 (tt) REVERT: A 39 GLU cc_start: 0.7825 (mp0) cc_final: 0.7571 (mp0) REVERT: A 120 GLU cc_start: 0.6919 (mp0) cc_final: 0.6625 (mp0) REVERT: A 124 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7665 (mp-120) REVERT: A 235 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8758 (mp) REVERT: A 260 ASP cc_start: 0.7765 (t70) cc_final: 0.7246 (t70) REVERT: A 609 ASP cc_start: 0.7562 (t70) cc_final: 0.7199 (t0) REVERT: A 806 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7850 (mtt-85) REVERT: A 1281 ARG cc_start: 0.7476 (ptt90) cc_final: 0.7197 (ptt-90) REVERT: A 1337 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7322 (mm-30) REVERT: B 312 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7426 (tm-30) REVERT: B 315 LYS cc_start: 0.8633 (ttpt) cc_final: 0.8294 (mtpp) REVERT: B 320 ASP cc_start: 0.8086 (t70) cc_final: 0.7775 (t0) REVERT: B 332 ASP cc_start: 0.7569 (t0) cc_final: 0.7169 (t0) REVERT: B 336 ARG cc_start: 0.8373 (ptp-170) cc_final: 0.8083 (ptp-110) REVERT: B 353 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8284 (mtpm) REVERT: B 358 LYS cc_start: 0.8384 (mtmt) cc_final: 0.8115 (mtmt) REVERT: B 560 GLU cc_start: 0.7242 (mm-30) cc_final: 0.7009 (mm-30) REVERT: B 620 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7930 (mpp80) REVERT: B 868 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.6046 (tpp) REVERT: B 883 LEU cc_start: 0.8540 (mt) cc_final: 0.8318 (mm) REVERT: B 889 THR cc_start: 0.8712 (t) cc_final: 0.8351 (p) REVERT: C 26 ASP cc_start: 0.7117 (p0) cc_final: 0.6891 (p0) REVERT: C 79 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: C 152 GLU cc_start: 0.7379 (tt0) cc_final: 0.7167 (tt0) REVERT: D 34 GLN cc_start: 0.7643 (mt0) cc_final: 0.7059 (mt0) REVERT: D 37 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7152 (mp10) REVERT: D 61 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7392 (tm-30) REVERT: D 119 ARG cc_start: 0.8573 (mmt90) cc_final: 0.8340 (mmt-90) REVERT: D 155 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6603 (tpt-90) REVERT: D 157 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7972 (mm-40) REVERT: E 207 ARG cc_start: 0.7853 (ttm110) cc_final: 0.7608 (ttm-80) REVERT: G 33 GLU cc_start: 0.7252 (tt0) cc_final: 0.6871 (tt0) REVERT: G 53 ASN cc_start: 0.7705 (m-40) cc_final: 0.7435 (t0) REVERT: G 100 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7820 (mt-10) REVERT: G 167 TYR cc_start: 0.8719 (m-80) cc_final: 0.8437 (m-80) REVERT: H 37 LYS cc_start: 0.8572 (pttt) cc_final: 0.8371 (ptmt) REVERT: I 97 MET cc_start: 0.8780 (mtp) cc_final: 0.8418 (mtm) REVERT: K 54 ARG cc_start: 0.7518 (mmm160) cc_final: 0.7241 (mmm160) REVERT: K 55 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8466 (mtpt) REVERT: K 102 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8151 (ttmt) REVERT: M 193 GLN cc_start: 0.8856 (mt0) cc_final: 0.8611 (tt0) REVERT: O 121 MET cc_start: 0.7773 (ttp) cc_final: 0.7340 (ttm) REVERT: Q 364 SER cc_start: 0.8431 (t) cc_final: 0.8080 (m) REVERT: Q 373 TYR cc_start: 0.7771 (m-10) cc_final: 0.7558 (m-10) REVERT: W 144 ARG cc_start: 0.8221 (mmm160) cc_final: 0.7932 (mmm-85) REVERT: W 148 LEU cc_start: 0.8444 (mm) cc_final: 0.8210 (mp) REVERT: X 261 LYS cc_start: 0.8134 (tppt) cc_final: 0.7799 (mmmm) REVERT: X 320 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8436 (mp) outliers start: 194 outliers final: 92 residues processed: 1404 average time/residue: 1.5733 time to fit residues: 2883.0355 Evaluate side-chains 1356 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1252 time to evaluate : 6.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 76 MET Chi-restraints excluded: chain 0 residue 95 LYS Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 189 THR Chi-restraints excluded: chain 0 residue 309 THR Chi-restraints excluded: chain 0 residue 467 ASP Chi-restraints excluded: chain 0 residue 531 LYS Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 660 ARG Chi-restraints excluded: chain 0 residue 709 SER Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 301 ILE Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 489 VAL Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 2 residue 130 VAL Chi-restraints excluded: chain 2 residue 182 PHE Chi-restraints excluded: chain 2 residue 216 MET Chi-restraints excluded: chain 4 residue 125 LEU Chi-restraints excluded: chain 4 residue 138 LYS Chi-restraints excluded: chain 4 residue 266 ASN Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 315 HIS Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 332 THR Chi-restraints excluded: chain 7 residue 226 VAL Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 544 SER Chi-restraints excluded: chain 7 residue 702 ASN Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 806 ARG Chi-restraints excluded: chain A residue 880 LYS Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1415 SER Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 329 ILE Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 172 LEU Chi-restraints excluded: chain O residue 184 SER Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 353 GLU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 290 VAL Chi-restraints excluded: chain X residue 320 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 288 optimal weight: 20.0000 chunk 771 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 502 optimal weight: 0.0370 chunk 211 optimal weight: 6.9990 chunk 857 optimal weight: 30.0000 chunk 711 optimal weight: 6.9990 chunk 396 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 450 optimal weight: 4.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 164 ASN 2 55 ASN ** 4 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 ASN A 700 ASN A 926 GLN B 366 GLN B 513 GLN B 686 ASN E 32 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN I 90 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 290 GLN ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 HIS ** R 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 74504 Z= 0.414 Angle : 0.607 12.158 100935 Z= 0.313 Chirality : 0.045 0.219 11408 Planarity : 0.005 0.071 12645 Dihedral : 10.318 177.836 10640 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.93 % Allowed : 16.25 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.20 (0.09), residues: 8759 helix: 0.93 (0.09), residues: 3570 sheet: -0.09 (0.14), residues: 1296 loop : -0.44 (0.10), residues: 3893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 954 HIS 0.008 0.001 HIS A 659 PHE 0.033 0.002 PHE A 219 TYR 0.025 0.002 TYR 7 335 ARG 0.015 0.001 ARG 7 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1282 time to evaluate : 6.280 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 90 MET cc_start: 0.9075 (mmm) cc_final: 0.8644 (mmm) REVERT: 0 183 LYS cc_start: 0.8287 (ttmt) cc_final: 0.8014 (tppp) REVERT: 0 269 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6942 (tp30) REVERT: 0 270 ARG cc_start: 0.7887 (tpp80) cc_final: 0.7644 (tpp80) REVERT: 0 289 LEU cc_start: 0.9175 (mt) cc_final: 0.8800 (mt) REVERT: 0 327 ARG cc_start: 0.7458 (mmt180) cc_final: 0.7109 (mmt90) REVERT: 0 352 ILE cc_start: 0.8746 (mt) cc_final: 0.8522 (mm) REVERT: 0 581 LEU cc_start: 0.8844 (mp) cc_final: 0.8499 (mm) REVERT: 0 660 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7410 (ptm160) REVERT: 1 87 HIS cc_start: 0.8681 (m-70) cc_final: 0.8339 (m-70) REVERT: 1 118 GLU cc_start: 0.7759 (tp30) cc_final: 0.7488 (tm-30) REVERT: 1 192 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7993 (tpt) REVERT: 1 317 LEU cc_start: 0.8819 (tp) cc_final: 0.8556 (tp) REVERT: 1 634 PHE cc_start: 0.8257 (t80) cc_final: 0.7841 (t80) REVERT: 2 118 GLN cc_start: 0.8246 (mp10) cc_final: 0.6973 (mp10) REVERT: 2 198 SER cc_start: 0.8654 (t) cc_final: 0.8381 (m) REVERT: 2 227 MET cc_start: 0.8113 (tmm) cc_final: 0.7751 (tmm) REVERT: 2 416 LEU cc_start: 0.9095 (tt) cc_final: 0.8879 (tm) REVERT: 3 120 LEU cc_start: 0.8990 (tp) cc_final: 0.8724 (tt) REVERT: 6 230 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7874 (mtp85) REVERT: 6 398 PHE cc_start: 0.8221 (m-80) cc_final: 0.7734 (m-10) REVERT: 7 160 ILE cc_start: 0.8986 (pt) cc_final: 0.8568 (mm) REVERT: 7 174 LYS cc_start: 0.8509 (tttt) cc_final: 0.7858 (ttmm) REVERT: 7 329 ARG cc_start: 0.8599 (tpm170) cc_final: 0.8223 (tpt-90) REVERT: 7 493 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8600 (t) REVERT: 7 546 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8321 (mttp) REVERT: 7 633 GLN cc_start: 0.7429 (tm-30) cc_final: 0.7121 (tm-30) REVERT: 7 694 LYS cc_start: 0.8857 (tmtt) cc_final: 0.8409 (tmtm) REVERT: 7 832 LEU cc_start: 0.8732 (tp) cc_final: 0.8385 (tt) REVERT: A 4 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7663 (mt0) REVERT: A 235 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8780 (mp) REVERT: A 260 ASP cc_start: 0.7824 (t70) cc_final: 0.7399 (t70) REVERT: A 414 ASP cc_start: 0.7605 (t0) cc_final: 0.7284 (t70) REVERT: A 486 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: A 609 ASP cc_start: 0.7556 (t70) cc_final: 0.7250 (t70) REVERT: A 806 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7961 (mtt-85) REVERT: A 822 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7145 (tt0) REVERT: A 1143 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8499 (tm) REVERT: A 1281 ARG cc_start: 0.7482 (ptt90) cc_final: 0.7196 (ptt-90) REVERT: A 1337 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7372 (mm-30) REVERT: B 312 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7493 (tm-30) REVERT: B 315 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8413 (mtpp) REVERT: B 320 ASP cc_start: 0.8104 (t70) cc_final: 0.7801 (t0) REVERT: B 332 ASP cc_start: 0.7649 (t0) cc_final: 0.7183 (t0) REVERT: B 336 ARG cc_start: 0.8418 (ptp-170) cc_final: 0.8016 (ptp-110) REVERT: B 353 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8280 (mtpm) REVERT: B 358 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8131 (mtmt) REVERT: B 392 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7812 (mtt-85) REVERT: B 426 LYS cc_start: 0.8101 (mmtp) cc_final: 0.7849 (mmpt) REVERT: B 484 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.7956 (m-40) REVERT: B 560 GLU cc_start: 0.7256 (mm-30) cc_final: 0.7007 (mm-30) REVERT: B 620 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7883 (mpp80) REVERT: C 26 ASP cc_start: 0.7192 (p0) cc_final: 0.6938 (p0) REVERT: C 79 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7919 (mt0) REVERT: C 85 ASP cc_start: 0.7468 (m-30) cc_final: 0.6992 (m-30) REVERT: C 152 GLU cc_start: 0.7387 (tt0) cc_final: 0.7185 (tt0) REVERT: C 155 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8456 (pp) REVERT: D 61 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7443 (tm-30) REVERT: D 155 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6619 (tpt-90) REVERT: D 157 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7974 (mm-40) REVERT: E 52 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6795 (pmm-80) REVERT: G 1 MET cc_start: 0.8095 (tpp) cc_final: 0.7629 (tpt) REVERT: G 33 GLU cc_start: 0.7253 (tt0) cc_final: 0.6880 (tt0) REVERT: G 53 ASN cc_start: 0.7716 (m-40) cc_final: 0.7398 (t0) REVERT: G 100 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7936 (mt-10) REVERT: G 167 TYR cc_start: 0.8751 (m-80) cc_final: 0.8465 (m-80) REVERT: H 37 LYS cc_start: 0.8580 (pttt) cc_final: 0.8373 (ptmt) REVERT: I 97 MET cc_start: 0.8786 (mtp) cc_final: 0.8414 (mtm) REVERT: K 54 ARG cc_start: 0.7571 (mmm160) cc_final: 0.7328 (mmm160) REVERT: K 55 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8479 (mtpt) REVERT: K 102 LYS cc_start: 0.8513 (ttpt) cc_final: 0.8181 (ttmt) REVERT: O 111 THR cc_start: 0.8759 (p) cc_final: 0.8484 (p) REVERT: O 129 GLU cc_start: 0.7924 (mp0) cc_final: 0.7279 (mp0) REVERT: O 139 TYR cc_start: 0.8732 (m-80) cc_final: 0.8451 (m-80) REVERT: Q 364 SER cc_start: 0.8487 (t) cc_final: 0.8125 (m) REVERT: R 268 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7519 (mtp) REVERT: X 261 LYS cc_start: 0.8207 (tppt) cc_final: 0.7865 (mmmm) REVERT: X 320 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8445 (mp) outliers start: 233 outliers final: 128 residues processed: 1402 average time/residue: 1.5901 time to fit residues: 2908.4418 Evaluate side-chains 1411 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1264 time to evaluate : 6.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 76 MET Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 189 THR Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 309 THR Chi-restraints excluded: chain 0 residue 366 LEU Chi-restraints excluded: chain 0 residue 377 CYS Chi-restraints excluded: chain 0 residue 467 ASP Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 625 ILE Chi-restraints excluded: chain 0 residue 660 ARG Chi-restraints excluded: chain 0 residue 709 SER Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 301 ILE Chi-restraints excluded: chain 1 residue 349 VAL Chi-restraints excluded: chain 1 residue 368 SER Chi-restraints excluded: chain 1 residue 374 ILE Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 489 VAL Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 2 residue 120 SER Chi-restraints excluded: chain 2 residue 182 PHE Chi-restraints excluded: chain 2 residue 216 MET Chi-restraints excluded: chain 2 residue 433 LEU Chi-restraints excluded: chain 3 residue 103 LEU Chi-restraints excluded: chain 4 residue 125 LEU Chi-restraints excluded: chain 4 residue 138 LYS Chi-restraints excluded: chain 4 residue 204 THR Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 6 residue 174 MET Chi-restraints excluded: chain 6 residue 230 ARG Chi-restraints excluded: chain 6 residue 332 THR Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain 6 residue 423 THR Chi-restraints excluded: chain 7 residue 154 GLN Chi-restraints excluded: chain 7 residue 226 VAL Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 493 VAL Chi-restraints excluded: chain 7 residue 544 SER Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 806 ARG Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 880 LYS Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 974 ASP Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 329 ILE Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 136 SER Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 172 LEU Chi-restraints excluded: chain O residue 184 SER Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 353 GLU Chi-restraints excluded: chain Q residue 375 LEU Chi-restraints excluded: chain R residue 268 MET Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 290 VAL Chi-restraints excluded: chain X residue 209 ASP Chi-restraints excluded: chain X residue 320 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 826 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 488 optimal weight: 9.9990 chunk 626 optimal weight: 5.9990 chunk 485 optimal weight: 4.9990 chunk 721 optimal weight: 0.9980 chunk 478 optimal weight: 0.0870 chunk 853 optimal weight: 4.9990 chunk 534 optimal weight: 0.6980 chunk 520 optimal weight: 4.9990 chunk 394 optimal weight: 0.5980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 164 ASN 0 365 GLN 1 493 ASN 2 165 ASN 3 90 ASN 4 303 ASN A 390 GLN A 700 ASN A 926 GLN B 366 GLN B 449 ASN B 513 GLN B 686 ASN B1013 ASN B1176 ASN D 34 GLN E 32 GLN G 131 GLN H 134 ASN I 90 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 290 GLN ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 74504 Z= 0.177 Angle : 0.531 12.549 100935 Z= 0.275 Chirality : 0.041 0.167 11408 Planarity : 0.004 0.063 12645 Dihedral : 10.200 178.437 10640 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.28 % Allowed : 17.47 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.42 (0.09), residues: 8759 helix: 1.14 (0.09), residues: 3564 sheet: -0.03 (0.14), residues: 1305 loop : -0.34 (0.10), residues: 3890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 192 HIS 0.010 0.001 HIS A 975 PHE 0.029 0.001 PHE W 228 TYR 0.022 0.001 TYR 7 335 ARG 0.019 0.000 ARG 7 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1450 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1269 time to evaluate : 6.355 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 90 MET cc_start: 0.9092 (mmm) cc_final: 0.8653 (mmm) REVERT: 0 183 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7999 (tppp) REVERT: 0 269 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6906 (tp30) REVERT: 0 289 LEU cc_start: 0.9166 (mt) cc_final: 0.8789 (mt) REVERT: 0 352 ILE cc_start: 0.8723 (mt) cc_final: 0.8470 (mm) REVERT: 0 427 ASN cc_start: 0.7534 (t0) cc_final: 0.7219 (p0) REVERT: 0 581 LEU cc_start: 0.8812 (mp) cc_final: 0.8481 (mm) REVERT: 0 660 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7355 (ptm160) REVERT: 1 87 HIS cc_start: 0.8660 (m-70) cc_final: 0.8291 (m-70) REVERT: 1 192 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7992 (tpt) REVERT: 1 343 ILE cc_start: 0.8654 (pt) cc_final: 0.8304 (mp) REVERT: 1 633 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6839 (t80) REVERT: 1 634 PHE cc_start: 0.8266 (t80) cc_final: 0.7867 (t80) REVERT: 1 636 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6570 (mp0) REVERT: 2 198 SER cc_start: 0.8609 (t) cc_final: 0.8349 (m) REVERT: 2 227 MET cc_start: 0.8103 (tmm) cc_final: 0.7664 (tmm) REVERT: 2 416 LEU cc_start: 0.9083 (tt) cc_final: 0.8870 (tm) REVERT: 3 120 LEU cc_start: 0.8962 (tp) cc_final: 0.8693 (tt) REVERT: 6 230 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7751 (mtp85) REVERT: 6 398 PHE cc_start: 0.8165 (m-80) cc_final: 0.7736 (m-10) REVERT: 7 160 ILE cc_start: 0.8965 (pt) cc_final: 0.8601 (mm) REVERT: 7 174 LYS cc_start: 0.8482 (tttt) cc_final: 0.7822 (ttmm) REVERT: 7 329 ARG cc_start: 0.8612 (tpm170) cc_final: 0.8230 (tpt-90) REVERT: 7 404 LYS cc_start: 0.8638 (mttt) cc_final: 0.8372 (mmtm) REVERT: 7 472 LYS cc_start: 0.7811 (mmtp) cc_final: 0.7541 (mmtm) REVERT: 7 493 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8483 (t) REVERT: 7 633 GLN cc_start: 0.7260 (tm-30) cc_final: 0.6893 (tm-30) REVERT: 7 694 LYS cc_start: 0.8819 (tmtt) cc_final: 0.8357 (tmtm) REVERT: 7 832 LEU cc_start: 0.8663 (tp) cc_final: 0.8336 (tt) REVERT: A 4 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7555 (mt0) REVERT: A 124 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7646 (mp-120) REVERT: A 235 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8752 (mp) REVERT: A 260 ASP cc_start: 0.7732 (t70) cc_final: 0.7379 (t70) REVERT: A 437 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7490 (mmm) REVERT: A 486 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7652 (mt-10) REVERT: A 526 ASP cc_start: 0.7554 (m-30) cc_final: 0.7172 (t0) REVERT: A 609 ASP cc_start: 0.7544 (t70) cc_final: 0.7190 (t0) REVERT: A 724 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7265 (tp30) REVERT: A 806 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7870 (mtt-85) REVERT: A 1143 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8424 (tm) REVERT: A 1281 ARG cc_start: 0.7477 (ptt90) cc_final: 0.7191 (ptt-90) REVERT: A 1337 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7314 (mm-30) REVERT: A 1444 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8004 (mmm) REVERT: B 312 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7392 (tm-30) REVERT: B 315 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8350 (mtpp) REVERT: B 320 ASP cc_start: 0.8079 (t70) cc_final: 0.7765 (t0) REVERT: B 332 ASP cc_start: 0.7587 (t0) cc_final: 0.7158 (t0) REVERT: B 336 ARG cc_start: 0.8340 (ptp-170) cc_final: 0.8061 (ptp-110) REVERT: B 353 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8285 (mtpm) REVERT: B 358 LYS cc_start: 0.8285 (mtmt) cc_final: 0.7897 (mtmt) REVERT: B 426 LYS cc_start: 0.7991 (mmtp) cc_final: 0.7758 (mmpt) REVERT: B 484 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7850 (m-40) REVERT: B 560 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6983 (mm-30) REVERT: B 620 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7859 (mpp80) REVERT: B 883 LEU cc_start: 0.8558 (mt) cc_final: 0.8322 (mm) REVERT: B 889 THR cc_start: 0.8691 (t) cc_final: 0.8326 (p) REVERT: C 26 ASP cc_start: 0.7108 (p0) cc_final: 0.6873 (p0) REVERT: C 79 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: D 61 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7391 (tm-30) REVERT: D 155 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6582 (tpt-90) REVERT: D 157 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7965 (mm-40) REVERT: E 52 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6663 (pmm-80) REVERT: G 53 ASN cc_start: 0.7663 (m-40) cc_final: 0.7436 (t0) REVERT: G 100 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7922 (mt-10) REVERT: G 167 TYR cc_start: 0.8723 (m-80) cc_final: 0.8438 (m-80) REVERT: I 92 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7355 (ptp-110) REVERT: I 97 MET cc_start: 0.8775 (mtp) cc_final: 0.8416 (mtm) REVERT: K 54 ARG cc_start: 0.7506 (mmm160) cc_final: 0.7232 (mmm160) REVERT: K 55 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8479 (mtpt) REVERT: M 182 ARG cc_start: 0.7709 (tpp80) cc_final: 0.6564 (tpp80) REVERT: M 193 GLN cc_start: 0.8867 (mt0) cc_final: 0.8639 (tt0) REVERT: O 111 THR cc_start: 0.8652 (p) cc_final: 0.8381 (p) REVERT: O 139 TYR cc_start: 0.8680 (m-80) cc_final: 0.8439 (m-80) REVERT: Q 364 SER cc_start: 0.8438 (t) cc_final: 0.8125 (m) REVERT: W 148 LEU cc_start: 0.8403 (mm) cc_final: 0.8156 (mp) REVERT: W 220 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7558 (p0) REVERT: X 214 TRP cc_start: 0.7615 (t60) cc_final: 0.7397 (t60) REVERT: X 261 LYS cc_start: 0.8141 (tppt) cc_final: 0.7803 (mmmm) REVERT: X 320 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8448 (mp) outliers start: 181 outliers final: 100 residues processed: 1368 average time/residue: 1.6415 time to fit residues: 2993.4744 Evaluate side-chains 1369 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1248 time to evaluate : 6.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 76 MET Chi-restraints excluded: chain 0 residue 189 THR Chi-restraints excluded: chain 0 residue 309 THR Chi-restraints excluded: chain 0 residue 467 ASP Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 625 ILE Chi-restraints excluded: chain 0 residue 660 ARG Chi-restraints excluded: chain 0 residue 709 SER Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 349 VAL Chi-restraints excluded: chain 1 residue 368 SER Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 489 VAL Chi-restraints excluded: chain 1 residue 493 ASN Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 1 residue 633 TYR Chi-restraints excluded: chain 2 residue 182 PHE Chi-restraints excluded: chain 2 residue 433 LEU Chi-restraints excluded: chain 4 residue 125 LEU Chi-restraints excluded: chain 4 residue 204 THR Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 315 HIS Chi-restraints excluded: chain 6 residue 230 ARG Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 332 THR Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain 7 residue 154 GLN Chi-restraints excluded: chain 7 residue 226 VAL Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 493 VAL Chi-restraints excluded: chain 7 residue 544 SER Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 806 ARG Chi-restraints excluded: chain A residue 880 LYS Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 329 ILE Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 172 LEU Chi-restraints excluded: chain O residue 184 SER Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain Q residue 353 GLU Chi-restraints excluded: chain Q residue 375 LEU Chi-restraints excluded: chain R residue 314 SER Chi-restraints excluded: chain U residue 262 LEU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain W residue 290 VAL Chi-restraints excluded: chain X residue 169 ILE Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain X residue 320 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 528 optimal weight: 3.9990 chunk 341 optimal weight: 2.9990 chunk 510 optimal weight: 0.7980 chunk 257 optimal weight: 10.0000 chunk 167 optimal weight: 40.0000 chunk 165 optimal weight: 9.9990 chunk 542 optimal weight: 0.9980 chunk 581 optimal weight: 3.9990 chunk 422 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 671 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 164 ASN 0 365 GLN ** 4 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN A 700 ASN A 926 GLN B 513 GLN B 592 ASN B 686 ASN D 34 GLN E 32 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN H 134 ASN I 90 GLN ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 74504 Z= 0.243 Angle : 0.554 11.822 100935 Z= 0.286 Chirality : 0.042 0.179 11408 Planarity : 0.004 0.079 12645 Dihedral : 10.194 178.262 10640 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.17 % Allowed : 18.12 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.45 (0.09), residues: 8759 helix: 1.16 (0.09), residues: 3558 sheet: 0.00 (0.14), residues: 1308 loop : -0.31 (0.10), residues: 3893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 954 HIS 0.006 0.001 HIS A 659 PHE 0.031 0.002 PHE 4 191 TYR 0.026 0.001 TYR 1 117 ARG 0.015 0.000 ARG 0 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1451 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1279 time to evaluate : 6.300 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 90 MET cc_start: 0.9086 (mmm) cc_final: 0.8671 (mmm) REVERT: 0 183 LYS cc_start: 0.8284 (ttmt) cc_final: 0.8006 (tppp) REVERT: 0 269 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6896 (tp30) REVERT: 0 270 ARG cc_start: 0.8141 (mmm160) cc_final: 0.7535 (tpp80) REVERT: 0 289 LEU cc_start: 0.9180 (mt) cc_final: 0.8817 (mt) REVERT: 0 352 ILE cc_start: 0.8734 (mt) cc_final: 0.8484 (mm) REVERT: 0 427 ASN cc_start: 0.7515 (t0) cc_final: 0.7208 (p0) REVERT: 0 581 LEU cc_start: 0.8817 (mp) cc_final: 0.8475 (mm) REVERT: 0 660 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7415 (ptm160) REVERT: 1 87 HIS cc_start: 0.8648 (m-70) cc_final: 0.8242 (m-70) REVERT: 1 192 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8013 (tpt) REVERT: 1 317 LEU cc_start: 0.8796 (tp) cc_final: 0.8581 (tp) REVERT: 1 633 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6803 (t80) REVERT: 1 634 PHE cc_start: 0.8275 (t80) cc_final: 0.7852 (t80) REVERT: 2 198 SER cc_start: 0.8612 (t) cc_final: 0.8347 (m) REVERT: 2 227 MET cc_start: 0.8097 (tmm) cc_final: 0.7669 (tmm) REVERT: 3 120 LEU cc_start: 0.8972 (tp) cc_final: 0.8709 (tt) REVERT: 6 230 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7815 (mtp85) REVERT: 6 398 PHE cc_start: 0.8228 (m-80) cc_final: 0.7784 (m-10) REVERT: 7 160 ILE cc_start: 0.8952 (pt) cc_final: 0.8615 (mm) REVERT: 7 174 LYS cc_start: 0.8455 (tttt) cc_final: 0.7986 (ttmm) REVERT: 7 199 ARG cc_start: 0.7583 (mtm110) cc_final: 0.7311 (mtm180) REVERT: 7 329 ARG cc_start: 0.8637 (tpm170) cc_final: 0.8242 (tpt-90) REVERT: 7 404 LYS cc_start: 0.8641 (mttt) cc_final: 0.8375 (mmtm) REVERT: 7 472 LYS cc_start: 0.7814 (mmtp) cc_final: 0.7542 (mmtm) REVERT: 7 493 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8486 (t) REVERT: 7 633 GLN cc_start: 0.7492 (tm-30) cc_final: 0.7107 (tm-30) REVERT: 7 637 MET cc_start: 0.7534 (tpp) cc_final: 0.7254 (mmm) REVERT: 7 694 LYS cc_start: 0.8826 (tmtt) cc_final: 0.8327 (tmtm) REVERT: 7 832 LEU cc_start: 0.8677 (tp) cc_final: 0.8343 (tt) REVERT: A 4 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7536 (mt0) REVERT: A 235 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8764 (mp) REVERT: A 260 ASP cc_start: 0.7773 (t70) cc_final: 0.7367 (t70) REVERT: A 437 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7476 (mmm) REVERT: A 486 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7709 (mt-10) REVERT: A 526 ASP cc_start: 0.7631 (m-30) cc_final: 0.7227 (t0) REVERT: A 609 ASP cc_start: 0.7551 (t70) cc_final: 0.7188 (t0) REVERT: A 806 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7935 (mtt-85) REVERT: A 1143 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8421 (tm) REVERT: A 1281 ARG cc_start: 0.7482 (ptt90) cc_final: 0.7109 (ptm-80) REVERT: A 1309 ASP cc_start: 0.8100 (m-30) cc_final: 0.7713 (m-30) REVERT: A 1337 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7341 (mm-30) REVERT: A 1444 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8047 (mmm) REVERT: B 312 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7390 (tm-30) REVERT: B 313 MET cc_start: 0.8456 (ttm) cc_final: 0.8172 (mtm) REVERT: B 315 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8453 (mtpp) REVERT: B 320 ASP cc_start: 0.8081 (t70) cc_final: 0.7775 (t0) REVERT: B 332 ASP cc_start: 0.7599 (t0) cc_final: 0.7182 (t0) REVERT: B 336 ARG cc_start: 0.8374 (ptp-170) cc_final: 0.7994 (ptp-110) REVERT: B 353 LYS cc_start: 0.8590 (ttmt) cc_final: 0.8297 (mtpm) REVERT: B 358 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7817 (mttt) REVERT: B 392 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7823 (mtt-85) REVERT: B 426 LYS cc_start: 0.7984 (mmtp) cc_final: 0.7761 (mmpt) REVERT: B 484 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.7916 (m-40) REVERT: B 560 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6973 (mm-30) REVERT: B 620 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7845 (mpp80) REVERT: B 883 LEU cc_start: 0.8571 (mt) cc_final: 0.8329 (mm) REVERT: B 889 THR cc_start: 0.8638 (t) cc_final: 0.8307 (p) REVERT: C 26 ASP cc_start: 0.7143 (p0) cc_final: 0.6889 (p0) REVERT: C 79 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7933 (mt0) REVERT: D 61 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7431 (tm-30) REVERT: D 155 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6603 (tpt-90) REVERT: D 157 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7936 (mm-40) REVERT: E 121 MET cc_start: 0.8172 (mmm) cc_final: 0.7899 (mmm) REVERT: E 177 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7890 (mtt90) REVERT: E 207 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7698 (ttm-80) REVERT: G 53 ASN cc_start: 0.7616 (m-40) cc_final: 0.7377 (t0) REVERT: G 100 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7946 (mt-10) REVERT: G 167 TYR cc_start: 0.8740 (m-80) cc_final: 0.8485 (m-80) REVERT: I 92 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7349 (ptp-110) REVERT: I 97 MET cc_start: 0.8785 (mtp) cc_final: 0.8430 (mtm) REVERT: K 54 ARG cc_start: 0.7507 (mmm160) cc_final: 0.7225 (mmm160) REVERT: K 55 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8482 (mtpt) REVERT: K 102 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8257 (tttp) REVERT: M 230 MET cc_start: 0.5464 (tpp) cc_final: 0.4636 (mpm) REVERT: O 79 ARG cc_start: 0.7248 (mmm-85) cc_final: 0.7028 (ttt90) REVERT: O 111 THR cc_start: 0.8653 (p) cc_final: 0.8382 (p) REVERT: O 139 TYR cc_start: 0.8679 (m-80) cc_final: 0.8444 (m-80) REVERT: Q 34 MET cc_start: 0.4722 (ttm) cc_final: 0.4394 (ttm) REVERT: Q 364 SER cc_start: 0.8474 (t) cc_final: 0.8154 (m) REVERT: R 122 LEU cc_start: 0.8760 (mp) cc_final: 0.8534 (mm) REVERT: R 319 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7733 (tptp) REVERT: W 80 LYS cc_start: 0.7713 (tptp) cc_final: 0.7448 (tptt) REVERT: W 148 LEU cc_start: 0.8397 (mm) cc_final: 0.8138 (mp) REVERT: W 220 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7601 (p0) REVERT: X 214 TRP cc_start: 0.7736 (t60) cc_final: 0.7524 (t60) REVERT: X 261 LYS cc_start: 0.8175 (tppt) cc_final: 0.7857 (mmmm) REVERT: X 320 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8439 (mp) outliers start: 172 outliers final: 105 residues processed: 1369 average time/residue: 1.5946 time to fit residues: 2848.1686 Evaluate side-chains 1390 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1264 time to evaluate : 6.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 76 MET Chi-restraints excluded: chain 0 residue 189 THR Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 467 ASP Chi-restraints excluded: chain 0 residue 472 MET Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 625 ILE Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 660 ARG Chi-restraints excluded: chain 0 residue 709 SER Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 349 VAL Chi-restraints excluded: chain 1 residue 368 SER Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 489 VAL Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 1 residue 633 TYR Chi-restraints excluded: chain 2 residue 182 PHE Chi-restraints excluded: chain 2 residue 216 MET Chi-restraints excluded: chain 2 residue 433 LEU Chi-restraints excluded: chain 4 residue 125 LEU Chi-restraints excluded: chain 4 residue 204 THR Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 315 HIS Chi-restraints excluded: chain 5 residue 66 MET Chi-restraints excluded: chain 6 residue 230 ARG Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 332 THR Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain 6 residue 423 THR Chi-restraints excluded: chain 7 residue 154 GLN Chi-restraints excluded: chain 7 residue 226 VAL Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 493 VAL Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 806 ARG Chi-restraints excluded: chain A residue 880 LYS Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 974 ASP Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 329 ILE Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 136 SER Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 172 LEU Chi-restraints excluded: chain O residue 184 SER Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 353 GLU Chi-restraints excluded: chain R residue 265 HIS Chi-restraints excluded: chain R residue 319 LYS Chi-restraints excluded: chain U residue 262 LEU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain W residue 290 VAL Chi-restraints excluded: chain X residue 169 ILE Chi-restraints excluded: chain X residue 320 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 776 optimal weight: 8.9990 chunk 818 optimal weight: 0.3980 chunk 746 optimal weight: 20.0000 chunk 795 optimal weight: 0.2980 chunk 817 optimal weight: 20.0000 chunk 478 optimal weight: 20.0000 chunk 346 optimal weight: 1.9990 chunk 624 optimal weight: 0.0570 chunk 244 optimal weight: 5.9990 chunk 719 optimal weight: 5.9990 chunk 752 optimal weight: 0.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 164 ASN 3 90 ASN 4 68 ASN ** 4 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN A 700 ASN A 926 GLN A 969 GLN A1110 ASN B 236 HIS B 513 GLN B 592 ASN B 686 ASN B1176 ASN D 34 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN H 134 ASN ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 74504 Z= 0.184 Angle : 0.548 11.507 100935 Z= 0.281 Chirality : 0.041 0.308 11408 Planarity : 0.004 0.076 12645 Dihedral : 10.141 178.589 10640 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.96 % Allowed : 18.70 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.56 (0.09), residues: 8759 helix: 1.24 (0.09), residues: 3551 sheet: 0.09 (0.14), residues: 1283 loop : -0.25 (0.10), residues: 3925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 192 HIS 0.005 0.001 HIS B 984 PHE 0.033 0.001 PHE 4 191 TYR 0.022 0.001 TYR 4 235 ARG 0.014 0.000 ARG 7 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1440 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1284 time to evaluate : 6.312 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: symmetry clash revert: symmetry clash REVERT: 0 90 MET cc_start: 0.9076 (mmm) cc_final: 0.8757 (mmm) REVERT: 0 183 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7995 (tppp) REVERT: 0 269 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6894 (tp30) REVERT: 0 270 ARG cc_start: 0.8159 (mmm160) cc_final: 0.7542 (tpp80) REVERT: 0 289 LEU cc_start: 0.9165 (mt) cc_final: 0.8801 (mt) REVERT: 0 352 ILE cc_start: 0.8725 (mt) cc_final: 0.8476 (mm) REVERT: 0 419 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8894 (mm) REVERT: 0 427 ASN cc_start: 0.7536 (t0) cc_final: 0.7217 (p0) REVERT: 0 581 LEU cc_start: 0.8780 (mp) cc_final: 0.8446 (mm) REVERT: 0 660 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7169 (ptm160) REVERT: 1 87 HIS cc_start: 0.8666 (m-70) cc_final: 0.8032 (m170) REVERT: 1 192 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7966 (tpt) REVERT: 1 317 LEU cc_start: 0.8775 (tp) cc_final: 0.8558 (tp) REVERT: 1 349 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7773 (p) REVERT: 1 633 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6852 (t80) REVERT: 1 634 PHE cc_start: 0.8285 (t80) cc_final: 0.7866 (t80) REVERT: 1 636 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6566 (mp0) REVERT: 2 198 SER cc_start: 0.8593 (t) cc_final: 0.8336 (m) REVERT: 2 227 MET cc_start: 0.8076 (tmm) cc_final: 0.7646 (tmm) REVERT: 3 120 LEU cc_start: 0.8957 (tp) cc_final: 0.8690 (tt) REVERT: 4 138 LYS cc_start: 0.8663 (tmtp) cc_final: 0.8343 (tptp) REVERT: 4 281 ARG cc_start: 0.7054 (ptt90) cc_final: 0.6792 (ptt90) REVERT: 4 317 ILE cc_start: 0.7989 (pp) cc_final: 0.7702 (pp) REVERT: 6 230 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7782 (mtp85) REVERT: 6 398 PHE cc_start: 0.8195 (m-80) cc_final: 0.7711 (m-10) REVERT: 7 160 ILE cc_start: 0.8916 (pt) cc_final: 0.8639 (mm) REVERT: 7 174 LYS cc_start: 0.8426 (tttt) cc_final: 0.7947 (ttmm) REVERT: 7 199 ARG cc_start: 0.7595 (mtm110) cc_final: 0.7097 (mtm180) REVERT: 7 329 ARG cc_start: 0.8649 (tpm170) cc_final: 0.8238 (tpt-90) REVERT: 7 404 LYS cc_start: 0.8618 (mttt) cc_final: 0.8315 (mmtm) REVERT: 7 472 LYS cc_start: 0.7811 (mmtp) cc_final: 0.7536 (mmtm) REVERT: 7 493 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8411 (t) REVERT: 7 633 GLN cc_start: 0.7427 (tm-30) cc_final: 0.6748 (tm-30) REVERT: 7 637 MET cc_start: 0.7607 (tpp) cc_final: 0.7343 (tpp) REVERT: 7 694 LYS cc_start: 0.8802 (tmtt) cc_final: 0.8317 (tmtm) REVERT: 7 832 LEU cc_start: 0.8618 (tp) cc_final: 0.8281 (tt) REVERT: A 22 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.7620 (t80) REVERT: A 120 GLU cc_start: 0.6969 (mp0) cc_final: 0.6636 (mp0) REVERT: A 124 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7596 (mp-120) REVERT: A 235 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8739 (mp) REVERT: A 260 ASP cc_start: 0.7734 (t70) cc_final: 0.7357 (t70) REVERT: A 486 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7698 (mt-10) REVERT: A 609 ASP cc_start: 0.7541 (t70) cc_final: 0.7178 (t0) REVERT: A 806 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7879 (mtt-85) REVERT: A 1135 ARG cc_start: 0.8129 (ttt-90) cc_final: 0.7845 (ttp80) REVERT: A 1143 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8372 (tm) REVERT: A 1309 ASP cc_start: 0.8071 (m-30) cc_final: 0.7643 (m-30) REVERT: A 1337 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7311 (mm-30) REVERT: A 1444 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8010 (mmm) REVERT: B 312 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7327 (tm-30) REVERT: B 315 LYS cc_start: 0.8677 (ttpt) cc_final: 0.8434 (mtpp) REVERT: B 320 ASP cc_start: 0.8068 (t70) cc_final: 0.7751 (t0) REVERT: B 332 ASP cc_start: 0.7539 (t0) cc_final: 0.7335 (t0) REVERT: B 353 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8329 (mtpm) REVERT: B 392 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7919 (mtt-85) REVERT: B 426 LYS cc_start: 0.7965 (mmtp) cc_final: 0.7744 (mmpt) REVERT: B 484 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.7896 (m-40) REVERT: B 560 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6947 (mm-30) REVERT: B 620 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7812 (mpp80) REVERT: B 889 THR cc_start: 0.8640 (t) cc_final: 0.8313 (p) REVERT: C 26 ASP cc_start: 0.7104 (p0) cc_final: 0.6868 (p0) REVERT: C 79 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7955 (mt0) REVERT: C 249 ASP cc_start: 0.7087 (t70) cc_final: 0.6857 (t70) REVERT: D 61 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7392 (tm-30) REVERT: D 155 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6611 (tpt-90) REVERT: D 157 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7931 (mm-40) REVERT: E 52 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6617 (pmm-80) REVERT: E 121 MET cc_start: 0.8149 (mmm) cc_final: 0.7870 (mmm) REVERT: E 207 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7654 (ttm-80) REVERT: G 100 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7920 (mt-10) REVERT: G 167 TYR cc_start: 0.8733 (m-80) cc_final: 0.8475 (m-80) REVERT: I 92 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7293 (ptp-110) REVERT: I 97 MET cc_start: 0.8784 (mtp) cc_final: 0.8415 (mtm) REVERT: K 54 ARG cc_start: 0.7511 (mmm160) cc_final: 0.7234 (mmm160) REVERT: K 55 LYS cc_start: 0.8689 (mtmt) cc_final: 0.8468 (mtpt) REVERT: K 102 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8188 (ttmt) REVERT: L 65 VAL cc_start: 0.8969 (p) cc_final: 0.8677 (t) REVERT: M 103 ASP cc_start: 0.7303 (t0) cc_final: 0.7059 (t70) REVERT: M 135 MET cc_start: 0.7453 (tmm) cc_final: 0.7236 (tmm) REVERT: M 230 MET cc_start: 0.5108 (tpp) cc_final: 0.4455 (mpm) REVERT: O 111 THR cc_start: 0.8618 (p) cc_final: 0.8371 (p) REVERT: O 139 TYR cc_start: 0.8682 (m-80) cc_final: 0.8476 (m-80) REVERT: Q 34 MET cc_start: 0.4844 (ttm) cc_final: 0.4588 (ttm) REVERT: Q 364 SER cc_start: 0.8478 (t) cc_final: 0.8152 (m) REVERT: Q 373 TYR cc_start: 0.7774 (m-10) cc_final: 0.7554 (m-10) REVERT: R 122 LEU cc_start: 0.8756 (mp) cc_final: 0.8529 (mm) REVERT: R 319 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7687 (tptp) REVERT: W 51 LYS cc_start: 0.8284 (mtpp) cc_final: 0.8049 (mmmt) REVERT: W 80 LYS cc_start: 0.7667 (tptp) cc_final: 0.7389 (tptt) REVERT: W 83 GLU cc_start: 0.7581 (tt0) cc_final: 0.7358 (tm-30) REVERT: W 148 LEU cc_start: 0.8373 (mm) cc_final: 0.8120 (mp) REVERT: W 220 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7572 (p0) REVERT: X 261 LYS cc_start: 0.8130 (tppt) cc_final: 0.7823 (mmmm) REVERT: X 320 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8435 (mp) outliers start: 156 outliers final: 95 residues processed: 1368 average time/residue: 1.5502 time to fit residues: 2786.8027 Evaluate side-chains 1358 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1240 time to evaluate : 6.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 76 MET Chi-restraints excluded: chain 0 residue 182 LEU Chi-restraints excluded: chain 0 residue 189 THR Chi-restraints excluded: chain 0 residue 419 ILE Chi-restraints excluded: chain 0 residue 467 ASP Chi-restraints excluded: chain 0 residue 472 MET Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 625 ILE Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 660 ARG Chi-restraints excluded: chain 0 residue 709 SER Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 349 VAL Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 489 VAL Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 1 residue 633 TYR Chi-restraints excluded: chain 2 residue 182 PHE Chi-restraints excluded: chain 2 residue 433 LEU Chi-restraints excluded: chain 4 residue 204 THR Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 315 HIS Chi-restraints excluded: chain 5 residue 66 MET Chi-restraints excluded: chain 6 residue 230 ARG Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 332 THR Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain 7 residue 154 GLN Chi-restraints excluded: chain 7 residue 226 VAL Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 493 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 806 ARG Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 329 ILE Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 136 SER Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 184 SER Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 353 GLU Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 265 HIS Chi-restraints excluded: chain R residue 319 LYS Chi-restraints excluded: chain U residue 262 LEU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain W residue 290 VAL Chi-restraints excluded: chain X residue 169 ILE Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain X residue 320 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 793 optimal weight: 0.9990 chunk 522 optimal weight: 3.9990 chunk 841 optimal weight: 4.9990 chunk 513 optimal weight: 2.9990 chunk 399 optimal weight: 2.9990 chunk 584 optimal weight: 1.9990 chunk 882 optimal weight: 0.0980 chunk 812 optimal weight: 10.0000 chunk 702 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 542 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 164 ASN 1 365 ASN 4 68 ASN ** 4 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN A 700 ASN A 926 GLN A 969 GLN B 513 GLN B 592 ASN B 686 ASN B 932 HIS B 975 GLN D 34 GLN D 179 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN K 52 ASN ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 290 GLN ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 74504 Z= 0.207 Angle : 0.563 11.615 100935 Z= 0.289 Chirality : 0.042 0.250 11408 Planarity : 0.004 0.066 12645 Dihedral : 10.123 178.584 10640 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.71 % Allowed : 19.27 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.60 (0.09), residues: 8759 helix: 1.26 (0.09), residues: 3544 sheet: 0.14 (0.14), residues: 1273 loop : -0.22 (0.10), residues: 3942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 954 HIS 0.006 0.001 HIS A 659 PHE 0.032 0.001 PHE B 322 TYR 0.026 0.001 TYR 1 117 ARG 0.012 0.000 ARG O 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17518 Ramachandran restraints generated. 8759 Oldfield, 0 Emsley, 8759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1410 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1274 time to evaluate : 7.957 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: symmetry clash revert: symmetry clash REVERT: 0 90 MET cc_start: 0.9114 (mmm) cc_final: 0.8805 (mmm) REVERT: 0 183 LYS cc_start: 0.8271 (ttmt) cc_final: 0.8001 (tppp) REVERT: 0 269 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6947 (tp30) REVERT: 0 270 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7507 (tpp80) REVERT: 0 289 LEU cc_start: 0.9169 (mt) cc_final: 0.8802 (mt) REVERT: 0 352 ILE cc_start: 0.8727 (mt) cc_final: 0.8495 (mm) REVERT: 0 419 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8905 (mm) REVERT: 0 427 ASN cc_start: 0.7546 (t0) cc_final: 0.7212 (p0) REVERT: 0 468 MET cc_start: 0.8697 (ttm) cc_final: 0.8324 (ttp) REVERT: 0 581 LEU cc_start: 0.8782 (mp) cc_final: 0.8447 (mm) REVERT: 0 660 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7221 (ptm160) REVERT: 1 87 HIS cc_start: 0.8657 (m-70) cc_final: 0.8074 (m170) REVERT: 1 192 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7973 (tpt) REVERT: 1 317 LEU cc_start: 0.8750 (tp) cc_final: 0.8535 (tp) REVERT: 1 343 ILE cc_start: 0.8651 (pt) cc_final: 0.8318 (mp) REVERT: 1 634 PHE cc_start: 0.8292 (t80) cc_final: 0.7875 (t80) REVERT: 2 198 SER cc_start: 0.8585 (t) cc_final: 0.8347 (m) REVERT: 2 227 MET cc_start: 0.8042 (tmm) cc_final: 0.7613 (tmm) REVERT: 2 416 LEU cc_start: 0.9073 (tt) cc_final: 0.8857 (tm) REVERT: 3 120 LEU cc_start: 0.8962 (tp) cc_final: 0.8696 (tt) REVERT: 4 138 LYS cc_start: 0.8707 (tmtp) cc_final: 0.8345 (tptp) REVERT: 4 281 ARG cc_start: 0.7111 (ptt90) cc_final: 0.6873 (ptt90) REVERT: 4 317 ILE cc_start: 0.7992 (pp) cc_final: 0.7719 (pp) REVERT: 6 230 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7799 (mtp85) REVERT: 6 398 PHE cc_start: 0.8244 (m-80) cc_final: 0.7792 (m-10) REVERT: 7 160 ILE cc_start: 0.8878 (pt) cc_final: 0.8641 (mm) REVERT: 7 174 LYS cc_start: 0.8415 (tttt) cc_final: 0.7944 (ttmm) REVERT: 7 199 ARG cc_start: 0.7591 (mtm110) cc_final: 0.7071 (mtm180) REVERT: 7 329 ARG cc_start: 0.8657 (tpm170) cc_final: 0.8240 (tpt-90) REVERT: 7 404 LYS cc_start: 0.8584 (mttt) cc_final: 0.8306 (mmtm) REVERT: 7 472 LYS cc_start: 0.7810 (mmtp) cc_final: 0.7528 (mmtm) REVERT: 7 493 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8406 (t) REVERT: 7 633 GLN cc_start: 0.7406 (tm-30) cc_final: 0.6928 (tm-30) REVERT: 7 694 LYS cc_start: 0.8790 (tmtt) cc_final: 0.8322 (tmtm) REVERT: 7 832 LEU cc_start: 0.8619 (tp) cc_final: 0.8280 (tt) REVERT: A 235 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8743 (mp) REVERT: A 260 ASP cc_start: 0.7740 (t70) cc_final: 0.7385 (t70) REVERT: A 486 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7717 (mt-10) REVERT: A 609 ASP cc_start: 0.7544 (t70) cc_final: 0.7183 (t0) REVERT: A 806 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7887 (mtt-85) REVERT: A 1135 ARG cc_start: 0.8147 (ttt-90) cc_final: 0.7869 (ttp80) REVERT: A 1143 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8365 (tm) REVERT: A 1281 ARG cc_start: 0.7464 (ptt90) cc_final: 0.7194 (ptt-90) REVERT: A 1337 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7302 (mm-30) REVERT: B 320 ASP cc_start: 0.8071 (t70) cc_final: 0.7749 (t0) REVERT: B 332 ASP cc_start: 0.7510 (t0) cc_final: 0.7235 (t0) REVERT: B 336 ARG cc_start: 0.8305 (ptp-110) cc_final: 0.8096 (ptp-110) REVERT: B 353 LYS cc_start: 0.8590 (ttmt) cc_final: 0.8326 (mtpm) REVERT: B 392 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8000 (mtt-85) REVERT: B 393 LYS cc_start: 0.8172 (mttp) cc_final: 0.7948 (mttp) REVERT: B 426 LYS cc_start: 0.7889 (mmtp) cc_final: 0.7666 (mmpt) REVERT: B 484 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.7891 (m-40) REVERT: B 620 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7790 (mpp80) REVERT: B 662 MET cc_start: 0.8087 (mmm) cc_final: 0.7709 (mmm) REVERT: B 889 THR cc_start: 0.8661 (t) cc_final: 0.8338 (p) REVERT: C 26 ASP cc_start: 0.7103 (p0) cc_final: 0.6855 (p0) REVERT: C 79 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7960 (mt0) REVERT: C 249 ASP cc_start: 0.7138 (t70) cc_final: 0.6913 (t70) REVERT: D 61 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7371 (tm-30) REVERT: D 155 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6632 (tpt-90) REVERT: D 157 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7952 (mm-40) REVERT: E 207 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7622 (ttm-80) REVERT: G 100 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7918 (mt-10) REVERT: G 167 TYR cc_start: 0.8751 (m-80) cc_final: 0.8480 (m-80) REVERT: I 8 ARG cc_start: 0.7478 (ttp80) cc_final: 0.7186 (ttp80) REVERT: I 92 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7303 (ptp-110) REVERT: I 97 MET cc_start: 0.8785 (mtp) cc_final: 0.8461 (mtm) REVERT: K 54 ARG cc_start: 0.7490 (mmm160) cc_final: 0.7216 (mmm160) REVERT: K 55 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8469 (mtpt) REVERT: K 102 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8194 (tttp) REVERT: M 230 MET cc_start: 0.5040 (tpp) cc_final: 0.4532 (mpm) REVERT: O 79 ARG cc_start: 0.7275 (mmm-85) cc_final: 0.7012 (ttt90) REVERT: O 111 THR cc_start: 0.8621 (p) cc_final: 0.8403 (p) REVERT: O 141 ARG cc_start: 0.7937 (ttp-110) cc_final: 0.7734 (ttp-170) REVERT: Q 34 MET cc_start: 0.4848 (ttm) cc_final: 0.4609 (ttm) REVERT: Q 364 SER cc_start: 0.8492 (t) cc_final: 0.8172 (m) REVERT: Q 373 TYR cc_start: 0.7725 (m-10) cc_final: 0.7327 (m-10) REVERT: R 116 ILE cc_start: 0.9109 (pt) cc_final: 0.8888 (pp) REVERT: R 122 LEU cc_start: 0.8766 (mp) cc_final: 0.8539 (mm) REVERT: R 318 LEU cc_start: 0.8486 (pp) cc_final: 0.8067 (mt) REVERT: W 80 LYS cc_start: 0.7652 (tptp) cc_final: 0.7380 (tptt) REVERT: W 83 GLU cc_start: 0.7545 (tt0) cc_final: 0.7316 (tm-30) REVERT: W 148 LEU cc_start: 0.8365 (mm) cc_final: 0.8109 (mp) REVERT: W 220 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7549 (p0) REVERT: X 261 LYS cc_start: 0.8156 (tppt) cc_final: 0.7845 (mmmm) REVERT: X 320 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8427 (mp) outliers start: 136 outliers final: 99 residues processed: 1353 average time/residue: 1.5952 time to fit residues: 2835.1698 Evaluate side-chains 1373 residues out of total 7947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1258 time to evaluate : 6.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 76 MET Chi-restraints excluded: chain 0 residue 182 LEU Chi-restraints excluded: chain 0 residue 419 ILE Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 625 ILE Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 660 ARG Chi-restraints excluded: chain 0 residue 709 SER Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 349 VAL Chi-restraints excluded: chain 1 residue 374 ILE Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 489 VAL Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 2 residue 182 PHE Chi-restraints excluded: chain 2 residue 216 MET Chi-restraints excluded: chain 2 residue 433 LEU Chi-restraints excluded: chain 4 residue 204 THR Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 315 HIS Chi-restraints excluded: chain 6 residue 174 MET Chi-restraints excluded: chain 6 residue 230 ARG Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 332 THR Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain 6 residue 423 THR Chi-restraints excluded: chain 7 residue 226 VAL Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 493 VAL Chi-restraints excluded: chain 7 residue 675 SER Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 806 ARG Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 974 ASP Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 329 ILE Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 136 SER Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 184 SER Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 265 HIS Chi-restraints excluded: chain U residue 262 LEU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain W residue 190 ASP Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain W residue 290 VAL Chi-restraints excluded: chain X residue 169 ILE Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain X residue 320 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 430 optimal weight: 7.9990 chunk 558 optimal weight: 1.9990 chunk 748 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 648 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 704 optimal weight: 2.9990 chunk 294 optimal weight: 10.0000 chunk 722 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 365 GLN 4 68 ASN ** 4 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 740 HIS A 390 GLN A 700 ASN A 926 GLN A 969 GLN B 513 GLN B 592 ASN B 686 ASN D 34 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.197620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.153653 restraints weight = 83534.238| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.24 r_work: 0.3352 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 74504 Z= 0.317 Angle : 0.608 11.495 100935 Z= 0.310 Chirality : 0.044 0.275 11408 Planarity : 0.005 0.069 12645 Dihedral : 10.181 178.409 10640 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.78 % Allowed : 19.56 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.52 (0.09), residues: 8759 helix: 1.19 (0.09), residues: 3553 sheet: 0.06 (0.14), residues: 1301 loop : -0.24 (0.10), residues: 3905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 313 HIS 0.016 0.001 HIS A 975 PHE 0.034 0.002 PHE B 322 TYR 0.037 0.002 TYR 7 335 ARG 0.015 0.001 ARG 7 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37274.76 seconds wall clock time: 642 minutes 37.74 seconds (38557.74 seconds total)