Starting phenix.real_space_refine on Thu Mar 21 08:28:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bz1_16335/03_2024/8bz1_16335_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bz1_16335/03_2024/8bz1_16335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bz1_16335/03_2024/8bz1_16335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bz1_16335/03_2024/8bz1_16335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bz1_16335/03_2024/8bz1_16335_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bz1_16335/03_2024/8bz1_16335_neut.pdb" } resolution = 3.8 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= 1.000 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: 8 Type Number sf(0) Gaussians Zn 9 6.06 5 P 394 5.49 5 Mg 1 5.21 5 S 246 5.16 5 C 32423 2.51 5 N 9538 2.21 5 O 10768 1.98 5 H 50237 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 140": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 193": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 227": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 241": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 342": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 351": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 358": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 364": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 382": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 401": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 421": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 426": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 430": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 448": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 473": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 475": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 483": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 523": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 532": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 546": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 551": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 557": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 583": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 604": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 666": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 734": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 743": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 749": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 797": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 805": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 820": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 844": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 862": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 863": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 880": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 890": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 921": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 928": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 931": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 932": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 954": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 958": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 960": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 963": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 967": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 985": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 999": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1031": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1046": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1052": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1053": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1059": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1167": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1258": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1286": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1380": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1416": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1421": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 222": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 230": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 255": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 274": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 282": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 324": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 371": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 380": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 392": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 416": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 425": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 438": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 463": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 472": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 483": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 499": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 588": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 591": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 592": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 605": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 608": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 610": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 613": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 620": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 623": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 638": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 646": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 721": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 743": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 762": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 768": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 770": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 798": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 803": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 807": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 812": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 834": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 841": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 859": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 890": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 897": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 922": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 924": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 927": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 938": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 950": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1023": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1035": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1050": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1062": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1064": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1072": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1078": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1080": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1085": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1091": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 193": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 240": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 54": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 93": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 172": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 181": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 187": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 195": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 207": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 144": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 140": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 122": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 31": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 193": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 237": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 248": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 269": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 286": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 295": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 208": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 235": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 239": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 269": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 299": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 318": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 336": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 17": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 167": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 140": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 167": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 26": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 344": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 54": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 93": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 31": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 93": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 54": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 93": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 93": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 103616 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 22693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1423, 22693 Classifications: {'peptide': 1423} Link IDs: {'PCIS': 3, 'PTRANS': 67, 'TRANS': 1352} Chain breaks: 4 Chain: "B" Number of atoms: 18198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 18198 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1082} Chain breaks: 2 Chain: "C" Number of atoms: 4071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4071 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2084 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3459 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1351 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2710 Classifications: {'peptide': 171} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 2334 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1796 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1034 Classifications: {'peptide': 64} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1862 Classifications: {'peptide': 115} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 756 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 3945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 3945 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain breaks: 1 Chain: "N" Number of atoms: 6271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 6271 Classifications: {'DNA': 198} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 197} Chain: "O" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2937 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "Q" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2242 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3609 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "T" Number of atoms: 6280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 6280 Classifications: {'DNA': 198} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 197} Chain: "U" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1820 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "V" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1624 Classifications: {'peptide': 99} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "a" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1643 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1350 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "c" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1752 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "d" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1561 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "e" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1665 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "f" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1350 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "g" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1696 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "h" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1513 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 943 SG CYS A 71 123.513 65.841 96.013 1.00186.13 S ATOM 985 SG CYS A 74 121.042 63.068 97.172 1.00185.49 S ATOM 1073 SG CYS A 81 119.958 65.919 95.714 1.00178.38 S ATOM 1557 SG CYS A 111 100.471 68.494 139.158 1.00279.10 S ATOM 1608 SG CYS A 114 101.718 65.585 139.670 1.00275.55 S ATOM 2268 SG CYS A 154 98.340 66.915 142.207 1.00275.31 S ATOM 40005 SG CYS B1119 113.423 52.668 106.617 1.00182.77 S ATOM 40049 SG CYS B1122 112.476 56.139 108.102 1.00185.76 S ATOM 40275 SG CYS B1137 115.721 55.536 106.455 1.00191.82 S ATOM 40317 SG CYS B1140 114.949 54.017 109.900 1.00194.25 S ATOM 42297 SG CYS C 90 114.270 77.496 34.523 1.00103.69 S ATOM 42358 SG CYS C 94 114.615 79.815 32.389 1.00 85.17 S ATOM 42398 SG CYS C 97 111.324 79.468 34.373 1.00 79.51 S ATOM 56992 SG CYS I 17 51.881 124.521 129.129 1.00128.64 S ATOM 57035 SG CYS I 20 55.469 123.503 128.597 1.00129.86 S ATOM 57357 SG CYS I 39 53.250 120.889 129.301 1.00134.38 S ATOM 57406 SG CYS I 42 54.294 124.393 131.676 1.00136.00 S ATOM 58080 SG CYS I 86 33.144 120.675 88.265 1.00110.63 S ATOM 58130 SG CYS I 89 33.183 123.932 86.283 1.00112.07 S ATOM 58523 SG CYS I 114 36.252 121.911 86.248 1.00100.23 S ATOM 58589 SG CYS I 119 35.170 123.725 89.414 1.00112.09 S ATOM 58813 SG CYS J 7 83.322 91.554 41.682 1.00 32.89 S ATOM 58858 SG CYS J 10 82.916 89.459 38.481 1.00 35.01 S ATOM 59384 SG CYS J 44 79.884 90.255 40.815 1.00 38.47 S ATOM 59395 SG CYS J 45 81.454 92.651 38.347 1.00 37.41 S ATOM 61674 SG CYS L 19 114.588 114.326 62.112 1.00 71.88 S ATOM 61707 SG CYS L 22 115.627 116.082 59.396 1.00 76.19 S ATOM 61938 SG CYS L 36 118.131 115.520 62.288 1.00 83.72 S Time building chain proxies: 32.54, per 1000 atoms: 0.31 Number of scatterers: 103616 At special positions: 0 Unit cell: (182.7, 184.8, 263.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 9 29.99 S 246 16.00 P 394 15.00 Mg 1 11.99 O 10768 8.00 N 9538 7.00 C 32423 6.00 H 50237 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 72.46 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " 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 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" NE2 HIS M 18 " Number of angles added : 27 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10678 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 60 sheets defined 45.3% alpha, 15.2% beta 150 base pairs and 349 stacking pairs defined. Time for finding SS restraints: 39.23 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 removed outlier: 4.033A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.538A pdb=" N ILE A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.511A pdb=" N ASP A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.692A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 557 through 565 removed outlier: 3.612A pdb=" N MET A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.792A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.594A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.699A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLY A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 861 " --> pdb=" O THR A 857 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.849A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1102 removed outlier: 3.866A pdb=" N MET A1102 " --> pdb=" O ALA A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1186 through 1198 removed outlier: 3.608A pdb=" N GLN A1190 " --> pdb=" O VAL A1186 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.666A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1267 Processing helix chain 'A' and resid 1283 through 1293 removed outlier: 3.761A pdb=" N CYS A1287 " --> pdb=" O VAL A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1407 Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1432 removed outlier: 3.739A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 removed outlier: 3.548A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1460 Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1476 through 1482 removed outlier: 3.898A pdb=" N TYR A1482 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.493A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 246 through 253 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.896A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 309 Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.659A pdb=" N ALA B 459 " --> pdb=" O GLN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 491 through 496 removed outlier: 4.069A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 491 through 496' Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.759A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 removed outlier: 3.572A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.525A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 711 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 732 removed outlier: 3.842A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 removed outlier: 4.588A pdb=" N HIS B 741 " --> pdb=" O THR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.146A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.635A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1018 removed outlier: 3.606A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1059 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 71 Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.943A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.567A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.964A pdb=" N SER D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.675A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.927A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 removed outlier: 4.279A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 122 removed outlier: 3.775A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.860A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 21 through 26 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'I' and resid 63 through 68 removed outlier: 4.124A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.564A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.865A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'M' and resid 47 through 52 Processing helix chain 'M' and resid 108 through 128 removed outlier: 3.647A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 149 Processing helix chain 'M' and resid 155 through 171 Processing helix chain 'M' and resid 176 through 184 Processing helix chain 'M' and resid 187 through 203 Processing helix chain 'M' and resid 211 through 222 removed outlier: 3.737A pdb=" N MET M 215 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER M 216 " --> pdb=" O GLY M 212 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ARG M 217 " --> pdb=" O ASP M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 242 Processing helix chain 'M' and resid 249 through 265 Processing helix chain 'M' and resid 270 through 279 Processing helix chain 'M' and resid 281 through 293 Processing helix chain 'M' and resid 295 through 300 Processing helix chain 'M' and resid 309 through 313 Processing helix chain 'O' and resid 179 through 187 Processing helix chain 'O' and resid 226 through 244 Processing helix chain 'O' and resid 269 through 277 Processing helix chain 'O' and resid 317 through 335 removed outlier: 3.821A pdb=" N ILE O 321 " --> pdb=" O VAL O 317 " (cutoff:3.500A) Proline residue: O 330 - end of helix Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 34 through 36 No H-bonds generated for 'chain 'Q' and resid 34 through 36' Processing helix chain 'Q' and resid 156 through 164 Processing helix chain 'Q' and resid 165 through 170 removed outlier: 3.743A pdb=" N VAL Q 170 " --> pdb=" O ARG Q 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 180 removed outlier: 3.889A pdb=" N MET Q 177 " --> pdb=" O HIS Q 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 14 Processing helix chain 'R' and resid 25 through 34 Processing helix chain 'R' and resid 35 through 37 No H-bonds generated for 'chain 'R' and resid 35 through 37' Processing helix chain 'R' and resid 59 through 64 Processing helix chain 'R' and resid 123 through 137 removed outlier: 3.625A pdb=" N LEU R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 173 Processing helix chain 'R' and resid 179 through 194 removed outlier: 3.715A pdb=" N LYS R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 207 Processing helix chain 'R' and resid 209 through 221 removed outlier: 3.632A pdb=" N GLU R 219 " --> pdb=" O GLU R 215 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 33 removed outlier: 4.586A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 51 removed outlier: 4.020A pdb=" N LEU U 39 " --> pdb=" O ASP U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 325 through 330 Processing helix chain 'V' and resid 9 through 25 removed outlier: 3.856A pdb=" N LEU V 15 " --> pdb=" O LEU V 11 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 52 removed outlier: 3.801A pdb=" N ALA V 33 " --> pdb=" O THR V 29 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL V 52 " --> pdb=" O LEU V 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 58 Processing helix chain 'a' and resid 64 through 80 removed outlier: 4.112A pdb=" N ASP a 78 " --> pdb=" O GLU a 74 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE a 79 " --> pdb=" O ILE a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 115 Processing helix chain 'a' and resid 121 through 132 Processing helix chain 'b' and resid 26 through 30 Processing helix chain 'b' and resid 31 through 42 Processing helix chain 'b' and resid 50 through 77 Processing helix chain 'b' and resid 83 through 94 Processing helix chain 'c' and resid 17 through 23 Processing helix chain 'c' and resid 27 through 38 Processing helix chain 'c' and resid 46 through 74 removed outlier: 4.113A pdb=" N VAL c 50 " --> pdb=" O ALA c 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 91 Processing helix chain 'c' and resid 93 through 98 Processing helix chain 'c' and resid 113 through 117 Processing helix chain 'd' and resid 38 through 50 Processing helix chain 'd' and resid 56 through 85 Processing helix chain 'd' and resid 91 through 103 Processing helix chain 'd' and resid 105 through 125 removed outlier: 3.859A pdb=" N LYS d 109 " --> pdb=" O GLY d 105 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 58 Processing helix chain 'e' and resid 64 through 80 removed outlier: 3.502A pdb=" N ASP e 78 " --> pdb=" O GLU e 74 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE e 79 " --> pdb=" O ILE e 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 115 Processing helix chain 'e' and resid 121 through 132 removed outlier: 3.502A pdb=" N ILE e 125 " --> pdb=" O MET e 121 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 30 Processing helix chain 'f' and resid 31 through 42 Processing helix chain 'f' and resid 50 through 77 Processing helix chain 'f' and resid 83 through 95 Processing helix chain 'g' and resid 17 through 23 Processing helix chain 'g' and resid 27 through 38 Processing helix chain 'g' and resid 46 through 74 removed outlier: 4.082A pdb=" N VAL g 50 " --> pdb=" O ALA g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 80 through 91 Processing helix chain 'g' and resid 93 through 98 Processing helix chain 'h' and resid 38 through 50 Processing helix chain 'h' and resid 56 through 85 Processing helix chain 'h' and resid 91 through 103 Processing helix chain 'h' and resid 104 through 126 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.385A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 25 Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.530A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.620A pdb=" N ARG A 192 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.756A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.813A pdb=" N LYS A 357 " --> pdb=" O PHE B1086 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.881A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.925A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.707A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 554 through 556 Processing sheet with id=AB3, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.366A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.812A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB7, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB8, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB9, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.887A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.720A pdb=" N GLN A1299 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 3.868A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1319 through 1322 removed outlier: 3.674A pdb=" N LYS A1319 " --> pdb=" O LEU A1331 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1471 through 1475 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1471 through 1475 current: chain 'F' and resid 115 through 119 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 115 through 119 current: chain 'G' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 54 current: chain 'G' and resid 66 through 77 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.124A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.297A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.556A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 531 through 532 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 632 through 633 current: chain 'B' and resid 695 through 696 Processing sheet with id=AD2, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.319A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 747 through 751 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 808 through 818 current: chain 'B' and resid 902 through 911 removed outlier: 8.186A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 917 through 927 current: chain 'L' and resid 25 through 27 Processing sheet with id=AD4, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD5, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.118A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD7, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.755A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.303A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.530A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 113 through 116 removed outlier: 4.086A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 60 through 63 removed outlier: 6.526A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE4, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.907A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 117 through 119 Processing sheet with id=AE7, first strand: chain 'I' and resid 24 through 28 removed outlier: 3.975A pdb=" N TYR I 44 " --> pdb=" O CYS I 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE9, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF1, first strand: chain 'M' and resid 24 through 26 removed outlier: 3.605A pdb=" N MET M 32 " --> pdb=" O VAL M 41 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 190 through 192 removed outlier: 5.126A pdb=" N ILE O 168 " --> pdb=" O GLY O 223 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU O 165 " --> pdb=" O SER O 261 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N SER O 261 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR O 171 " --> pdb=" O ILE O 255 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE O 255 " --> pdb=" O THR O 171 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASN O 173 " --> pdb=" O PHE O 253 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE O 253 " --> pdb=" O ASN O 173 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 11 through 17 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 11 through 17 current: chain 'Q' and resid 98 through 102 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 109 through 114 current: chain 'Q' and resid 134 through 139 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 134 through 139 current: chain 'R' and resid 52 through 58 removed outlier: 10.074A pdb=" N THR R 52 " --> pdb=" O LEU R 85 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU R 85 " --> pdb=" O THR R 52 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL R 54 " --> pdb=" O PHE R 83 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 81 through 86 current: chain 'R' and resid 103 through 116 Processing sheet with id=AF4, first strand: chain 'R' and resid 196 through 198 removed outlier: 4.100A pdb=" N THR R 232 " --> pdb=" O ASN R 224 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 333 through 345 removed outlier: 3.653A pdb=" N ASP U 355 " --> pdb=" O GLN U 338 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASP U 340 " --> pdb=" O LEU U 353 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU U 353 " --> pdb=" O ASP U 340 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE U 342 " --> pdb=" O PHE U 351 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE U 351 " --> pdb=" O ILE U 342 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG U 344 " --> pdb=" O TRP U 349 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP U 349 " --> pdb=" O ARG U 344 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 363 through 367 current: chain 'V' and resid 55 through 64 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 55 through 64 current: chain 'V' and resid 71 through 83 removed outlier: 7.205A pdb=" N VAL V 71 " --> pdb=" O CYS V 98 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS V 98 " --> pdb=" O VAL V 71 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR V 73 " --> pdb=" O VAL V 96 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL V 96 " --> pdb=" O THR V 73 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL V 75 " --> pdb=" O LYS V 94 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS V 94 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN V 77 " --> pdb=" O LYS V 92 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS V 92 " --> pdb=" O ASN V 77 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 84 through 85 removed outlier: 6.839A pdb=" N ARG a 84 " --> pdb=" O VAL b 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'a' and resid 119 through 120 Processing sheet with id=AF8, first strand: chain 'b' and resid 98 through 99 Processing sheet with id=AF9, first strand: chain 'c' and resid 43 through 44 removed outlier: 7.030A pdb=" N ARG c 43 " --> pdb=" O ILE d 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'c' and resid 78 through 79 Processing sheet with id=AG2, first strand: chain 'c' and resid 101 through 103 Processing sheet with id=AG3, first strand: chain 'e' and resid 84 through 85 removed outlier: 6.842A pdb=" N ARG e 84 " --> pdb=" O VAL f 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'e' and resid 119 through 120 Processing sheet with id=AG5, first strand: chain 'g' and resid 43 through 44 removed outlier: 7.258A pdb=" N ARG g 43 " --> pdb=" O ILE h 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'g' and resid 78 through 79 2099 hydrogen bonds defined for protein. 5910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 389 hydrogen bonds 778 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 349 stacking parallelities Total time for adding SS restraints: 55.14 Time building geometry restraints manager: 75.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 50136 1.13 - 1.30: 8002 1.30 - 1.47: 22852 1.47 - 1.64: 24020 1.64 - 1.81: 392 Bond restraints: 105402 Sorted by residual: bond pdb=" N SER d 33 " pdb=" H SER d 33 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 bond pdb=" N ARG A 863 " pdb=" H ARG A 863 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" N ARG U 344 " pdb=" H ARG U 344 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" N SER h 33 " pdb=" H SER h 33 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.72e+01 bond pdb=" N ARG M 248 " pdb=" H ARG M 248 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.62e+01 ... (remaining 105397 not shown) Histogram of bond angle deviations from ideal: 91.60 - 102.21: 372 102.21 - 112.83: 124010 112.83 - 123.45: 62229 123.45 - 134.06: 4279 134.06 - 144.68: 13 Bond angle restraints: 190903 Sorted by residual: angle pdb=" C6 DA T -23 " pdb=" N6 DA T -23 " pdb=" H61 DA T -23 " ideal model delta sigma weight residual 120.00 91.60 28.40 1.50e+00 4.44e-01 3.59e+02 angle pdb=" C6 DA T -27 " pdb=" N6 DA T -27 " pdb=" H61 DA T -27 " ideal model delta sigma weight residual 120.00 92.50 27.50 1.50e+00 4.44e-01 3.36e+02 angle pdb=" C6 DA T -73 " pdb=" N6 DA T -73 " pdb=" H61 DA T -73 " ideal model delta sigma weight residual 120.00 93.53 26.47 1.50e+00 4.44e-01 3.12e+02 angle pdb=" C6 DA T -51 " pdb=" N6 DA T -51 " pdb=" H61 DA T -51 " ideal model delta sigma weight residual 120.00 93.91 26.09 1.50e+00 4.44e-01 3.02e+02 angle pdb=" C6 DA T-130 " pdb=" N6 DA T-130 " pdb=" H61 DA T-130 " ideal model delta sigma weight residual 120.00 144.68 -24.68 1.50e+00 4.44e-01 2.71e+02 ... (remaining 190898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 40249 17.96 - 35.93: 4272 35.93 - 53.89: 1970 53.89 - 71.86: 1051 71.86 - 89.82: 137 Dihedral angle restraints: 47679 sinusoidal: 28799 harmonic: 18880 Sorted by residual: dihedral pdb=" C GLU A 856 " pdb=" N GLU A 856 " pdb=" CA GLU A 856 " pdb=" CB GLU A 856 " ideal model delta harmonic sigma weight residual -122.60 -133.45 10.85 0 2.50e+00 1.60e-01 1.88e+01 dihedral pdb=" N GLU A 856 " pdb=" C GLU A 856 " pdb=" CA GLU A 856 " pdb=" CB GLU A 856 " ideal model delta harmonic sigma weight residual 122.80 131.74 -8.94 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" C SER B 719 " pdb=" N SER B 719 " pdb=" CA SER B 719 " pdb=" CB SER B 719 " ideal model delta harmonic sigma weight residual -122.60 -131.41 8.81 0 2.50e+00 1.60e-01 1.24e+01 ... (remaining 47676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 8068 0.100 - 0.201: 464 0.201 - 0.301: 12 0.301 - 0.401: 1 0.401 - 0.501: 2 Chirality restraints: 8547 Sorted by residual: chirality pdb=" C4' DA T -13 " pdb=" C5' DA T -13 " pdb=" O4' DA T -13 " pdb=" C3' DA T -13 " both_signs ideal model delta sigma weight residual False -2.53 -2.02 -0.50 2.00e-01 2.50e+01 6.29e+00 chirality pdb=" CA GLU A 856 " pdb=" N GLU A 856 " pdb=" C GLU A 856 " pdb=" CB GLU A 856 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA SER B 719 " pdb=" N SER B 719 " pdb=" C SER B 719 " pdb=" CB SER B 719 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 ... (remaining 8544 not shown) Planarity restraints: 14134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C6 DA T-117 " 0.083 2.00e-02 2.50e+03 2.02e-01 4.07e+02 pdb=" N6 DA T-117 " -0.348 2.00e-02 2.50e+03 pdb=" H61 DA T-117 " 0.131 2.00e-02 2.50e+03 pdb=" H62 DA T-117 " 0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 498 " 0.086 2.00e-02 2.50e+03 1.59e-01 2.54e+02 pdb=" N ASP A 499 " -0.276 2.00e-02 2.50e+03 pdb=" CA ASP A 499 " 0.085 2.00e-02 2.50e+03 pdb=" H ASP A 499 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 DA T -3 " 0.070 2.00e-02 2.50e+03 1.57e-01 2.48e+02 pdb=" N6 DA T -3 " -0.272 2.00e-02 2.50e+03 pdb=" H61 DA T -3 " 0.101 2.00e-02 2.50e+03 pdb=" H62 DA T -3 " 0.101 2.00e-02 2.50e+03 ... (remaining 14131 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.93: 2239 1.93 - 2.60: 108009 2.60 - 3.26: 316210 3.26 - 3.93: 430096 3.93 - 4.60: 648886 Nonbonded interactions: 1505440 Sorted by model distance: nonbonded pdb=" HE ARG B 385 " pdb=" OD1 ASP B 492 " model vdw 1.260 1.850 nonbonded pdb="HH22 ARG B 623 " pdb=" OE2 GLU B 697 " model vdw 1.297 1.850 nonbonded pdb=" OP1 DA T -44 " pdb=" HZ1 LYS e 38 " model vdw 1.303 1.850 nonbonded pdb=" OE2 GLU B 198 " pdb=" HZ1 LYS B 391 " model vdw 1.316 1.850 nonbonded pdb="HH22 ARG B 483 " pdb=" O ALA B 527 " model vdw 1.324 1.850 ... (remaining 1505435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'a' selection = (chain 'e' and resid 39 through 135) } ncs_group { reference = chain 'b' selection = chain 'f' } ncs_group { reference = (chain 'c' and resid 14 through 119) selection = chain 'g' } ncs_group { reference = (chain 'd' and resid 32 through 126) selection = chain 'h' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 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: 1.380 Extract box with map and model: 16.990 Check model and map are aligned: 1.140 Set scattering table: 0.740 Process input model: 324.170 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 352.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 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 : 0.004 0.051 55165 Z= 0.221 Angle : 0.737 9.723 76198 Z= 0.449 Chirality : 0.049 0.501 8547 Planarity : 0.009 0.113 8448 Dihedral : 18.097 89.821 21960 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.21 % 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: 0.10 (0.10), residues: 5591 helix: 0.32 (0.10), residues: 2311 sheet: 0.27 (0.17), residues: 826 loop : -0.09 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 49 HIS 0.023 0.001 HIS B 502 PHE 0.052 0.002 PHE A 837 TYR 0.114 0.005 TYR A 859 ARG 0.027 0.003 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 33 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Evaluate side-chains 627 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 627 time to evaluate : 5.766 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.7790 (ttp) cc_final: 0.7274 (tpt) REVERT: A 470 MET cc_start: 0.7750 (mtm) cc_final: 0.7331 (mtm) REVERT: A 625 ASP cc_start: 0.8280 (t0) cc_final: 0.7825 (t0) REVERT: A 900 SER cc_start: 0.8660 (m) cc_final: 0.8418 (p) REVERT: A 1102 MET cc_start: 0.4481 (mtt) cc_final: 0.2400 (mmm) REVERT: B 163 LEU cc_start: 0.8937 (mt) cc_final: 0.8510 (mt) REVERT: B 1041 ILE cc_start: 0.9152 (mm) cc_final: 0.8923 (mt) REVERT: G 7 LEU cc_start: 0.8568 (mt) cc_final: 0.8338 (mp) REVERT: M 116 ASN cc_start: 0.8544 (m-40) cc_final: 0.8255 (m110) REVERT: O 191 GLU cc_start: 0.9085 (pt0) cc_final: 0.8832 (pt0) REVERT: R 15 ASN cc_start: 0.8740 (m-40) cc_final: 0.8390 (p0) REVERT: V 1 MET cc_start: 0.2315 (ptm) cc_final: 0.1776 (mmt) REVERT: h 42 VAL cc_start: 0.8210 (t) cc_final: 0.7104 (t) outliers start: 0 outliers final: 0 residues processed: 627 average time/residue: 1.3718 time to fit residues: 1410.7649 Evaluate side-chains 376 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 5.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 498 optimal weight: 9.9990 chunk 447 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 238 optimal weight: 2.9990 chunk 462 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 281 optimal weight: 8.9990 chunk 344 optimal weight: 5.9990 chunk 535 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 HIS C 66 HIS D 76 ASN E 95 GLN E 108 GLN E 133 GLN H 133 HIS K 49 GLN Q 27 ASN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 76 HIS d 96 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 55165 Z= 0.385 Angle : 0.648 7.864 76198 Z= 0.376 Chirality : 0.043 0.171 8547 Planarity : 0.005 0.069 8448 Dihedral : 20.954 86.539 10519 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.89 % Allowed : 5.90 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % 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: 0.64 (0.11), residues: 5591 helix: 1.06 (0.10), residues: 2347 sheet: 0.14 (0.17), residues: 859 loop : 0.04 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 453 HIS 0.022 0.001 HIS I 100 PHE 0.022 0.002 PHE A 548 TYR 0.026 0.002 TYR h 41 ARG 0.007 0.001 ARG J 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 33 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Evaluate side-chains 408 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 364 time to evaluate : 5.835 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: -0.1961 (mtp) cc_final: -0.2288 (ppp) REVERT: A 769 MET cc_start: 0.8568 (mtm) cc_final: 0.8177 (mtm) REVERT: A 1102 MET cc_start: 0.4455 (mtt) cc_final: 0.2180 (tpt) REVERT: B 198 GLU cc_start: 0.6726 (tt0) cc_final: 0.6158 (mt-10) REVERT: B 785 TYR cc_start: 0.9297 (t80) cc_final: 0.8908 (t80) REVERT: E 91 CYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7627 (p) REVERT: G 7 LEU cc_start: 0.8544 (mt) cc_final: 0.8321 (mp) REVERT: G 104 MET cc_start: 0.4339 (tmm) cc_final: 0.4097 (tmm) REVERT: R 15 ASN cc_start: 0.8779 (m-40) cc_final: 0.8573 (m-40) REVERT: V 1 MET cc_start: 0.2015 (ptm) cc_final: 0.1406 (mmt) REVERT: V 58 PHE cc_start: 0.8799 (p90) cc_final: 0.8389 (p90) outliers start: 44 outliers final: 38 residues processed: 392 average time/residue: 1.2731 time to fit residues: 832.2302 Evaluate side-chains 350 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 311 time to evaluate : 5.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 968 ASN Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1145 GLN Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 33 PHE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 129 ASN Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 81 PHE Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain b residue 85 MET Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain d residue 66 PHE Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 95 GLU Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain f residue 75 GLU Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain h residue 95 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 297 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 445 optimal weight: 30.0000 chunk 364 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 536 optimal weight: 20.0000 chunk 579 optimal weight: 10.0000 chunk 478 optimal weight: 40.0000 chunk 532 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 430 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 277 HIS ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 32 HIS f 76 HIS g 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 55165 Z= 0.426 Angle : 0.679 9.059 76198 Z= 0.389 Chirality : 0.045 0.187 8547 Planarity : 0.005 0.084 8448 Dihedral : 21.935 92.467 10519 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 1.41 % Allowed : 6.73 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % 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: 0.16 (0.11), residues: 5591 helix: 0.80 (0.10), residues: 2336 sheet: -0.09 (0.17), residues: 845 loop : -0.39 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 453 HIS 0.017 0.002 HIS I 100 PHE 0.031 0.002 PHE d 66 TYR 0.036 0.003 TYR A1197 ARG 0.010 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 33 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Evaluate side-chains 390 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 320 time to evaluate : 6.444 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: -0.2103 (mtp) cc_final: -0.2325 (ppp) REVERT: A 467 MET cc_start: 0.7082 (mpp) cc_final: 0.6282 (mpp) REVERT: A 769 MET cc_start: 0.8548 (mtm) cc_final: 0.8283 (mtm) REVERT: A 854 THR cc_start: 0.7651 (m) cc_final: 0.7431 (p) REVERT: A 1007 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8272 (pt) REVERT: A 1102 MET cc_start: 0.3995 (mtt) cc_final: 0.1960 (tpt) REVERT: A 1451 MET cc_start: 0.4026 (tmm) cc_final: 0.3293 (tmm) REVERT: B 93 LEU cc_start: 0.8866 (tp) cc_final: 0.8536 (tt) REVERT: B 675 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7699 (mt) REVERT: C 66 HIS cc_start: 0.8888 (OUTLIER) cc_final: 0.8408 (t70) REVERT: E 91 CYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7624 (p) REVERT: F 127 ASP cc_start: 0.6211 (p0) cc_final: 0.5883 (p0) REVERT: G 7 LEU cc_start: 0.8736 (mt) cc_final: 0.8487 (mp) REVERT: M 190 GLU cc_start: 0.8058 (tp30) cc_final: 0.7724 (tm-30) REVERT: V 1 MET cc_start: 0.2172 (ptm) cc_final: 0.1454 (mmt) outliers start: 70 outliers final: 53 residues processed: 367 average time/residue: 1.2381 time to fit residues: 761.0919 Evaluate side-chains 351 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 294 time to evaluate : 5.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain B residue 1145 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 129 ASN Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 81 PHE Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 100 TYR Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain b residue 85 MET Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain d residue 66 PHE Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 95 GLU Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain f residue 75 GLU Chi-restraints excluded: chain g residue 59 LEU Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain h residue 63 MET Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 95 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 530 optimal weight: 9.9990 chunk 403 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 360 optimal weight: 40.0000 chunk 538 optimal weight: 20.0000 chunk 570 optimal weight: 6.9990 chunk 281 optimal weight: 40.0000 chunk 510 optimal weight: 40.0000 chunk 153 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 620 HIS ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN B1013 ASN ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 GLN d 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 55165 Z= 0.411 Angle : 0.641 10.271 76198 Z= 0.368 Chirality : 0.044 0.452 8547 Planarity : 0.005 0.064 8448 Dihedral : 22.157 93.754 10519 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.51 % Allowed : 8.12 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % 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: 0.09 (0.11), residues: 5591 helix: 0.86 (0.11), residues: 2333 sheet: -0.28 (0.17), residues: 849 loop : -0.49 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP V 72 HIS 0.013 0.001 HIS I 100 PHE 0.065 0.002 PHE A1239 TYR 0.027 0.002 TYR C 208 ARG 0.007 0.000 ARG M 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 33 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Evaluate side-chains 371 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 296 time to evaluate : 5.907 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: -0.2080 (mtp) cc_final: -0.2459 (ppp) REVERT: A 467 MET cc_start: 0.7033 (mpp) cc_final: 0.6372 (mpp) REVERT: A 769 MET cc_start: 0.8569 (mtm) cc_final: 0.8302 (mtm) REVERT: A 1007 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8376 (pt) REVERT: B 93 LEU cc_start: 0.8913 (tp) cc_final: 0.8528 (tt) REVERT: B 785 TYR cc_start: 0.9333 (t80) cc_final: 0.9111 (t80) REVERT: B 901 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8740 (p) REVERT: C 66 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8400 (t70) REVERT: E 91 CYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7670 (p) REVERT: F 127 ASP cc_start: 0.6286 (p0) cc_final: 0.5969 (p0) REVERT: G 7 LEU cc_start: 0.8841 (mt) cc_final: 0.8614 (mp) REVERT: G 104 MET cc_start: 0.4020 (tmm) cc_final: 0.3682 (tmm) REVERT: H 145 MET cc_start: 0.6611 (OUTLIER) cc_final: 0.6322 (mpp) REVERT: M 311 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7805 (p0) REVERT: O 202 MET cc_start: 0.9104 (mtp) cc_final: 0.8841 (mmm) REVERT: V 1 MET cc_start: 0.2185 (ptm) cc_final: 0.1464 (mmt) REVERT: g 63 ILE cc_start: 0.8030 (pt) cc_final: 0.7827 (tp) outliers start: 75 outliers final: 57 residues processed: 348 average time/residue: 1.1911 time to fit residues: 702.3676 Evaluate side-chains 347 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 284 time to evaluate : 5.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 968 ASN Chi-restraints excluded: chain B residue 1125 MET Chi-restraints excluded: chain B residue 1145 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 129 ASN Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain O residue 292 ILE Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 81 PHE Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 100 TYR Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain b residue 85 MET Chi-restraints excluded: chain c residue 59 LEU Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain d residue 66 PHE Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 95 GLU Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain e residue 121 MET Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain f residue 75 GLU Chi-restraints excluded: chain f residue 86 ASP Chi-restraints excluded: chain g residue 59 LEU Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain h residue 69 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 474 optimal weight: 40.0000 chunk 323 optimal weight: 20.0000 chunk 8 optimal weight: 50.0000 chunk 424 optimal weight: 10.0000 chunk 235 optimal weight: 0.9980 chunk 486 optimal weight: 10.0000 chunk 394 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 291 optimal weight: 10.0000 chunk 511 optimal weight: 30.0000 chunk 143 optimal weight: 3.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1291 ASN B 461 GLN B 790 GLN C 177 ASN ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 ASN R 123 ASN a 69 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 55165 Z= 0.421 Angle : 0.645 10.519 76198 Z= 0.370 Chirality : 0.044 0.213 8547 Planarity : 0.005 0.065 8448 Dihedral : 22.400 93.840 10519 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.67 % Allowed : 9.19 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % 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: -0.06 (0.11), residues: 5591 helix: 0.81 (0.11), residues: 2330 sheet: -0.43 (0.17), residues: 826 loop : -0.64 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 453 HIS 0.012 0.002 HIS K 40 PHE 0.019 0.002 PHE K 105 TYR 0.021 0.002 TYR H 142 ARG 0.006 0.001 ARG A 880 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 33 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 287 time to evaluate : 5.775 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: -0.1909 (mtp) cc_final: -0.2456 (ppp) REVERT: A 769 MET cc_start: 0.8504 (mtm) cc_final: 0.8269 (mtm) REVERT: B 93 LEU cc_start: 0.8979 (tp) cc_final: 0.8593 (tt) REVERT: B 176 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: B 1165 MET cc_start: 0.9068 (tpp) cc_final: 0.8662 (tpp) REVERT: C 66 HIS cc_start: 0.8861 (OUTLIER) cc_final: 0.8505 (t70) REVERT: E 91 CYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7734 (p) REVERT: F 127 ASP cc_start: 0.6557 (p0) cc_final: 0.6271 (p0) REVERT: G 7 LEU cc_start: 0.8839 (mt) cc_final: 0.8580 (mp) REVERT: G 104 MET cc_start: 0.4001 (tmm) cc_final: 0.3673 (tmm) REVERT: V 1 MET cc_start: 0.2142 (ptm) cc_final: 0.1403 (mmt) outliers start: 83 outliers final: 63 residues processed: 342 average time/residue: 1.2070 time to fit residues: 703.8892 Evaluate side-chains 342 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 276 time to evaluate : 5.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1145 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 129 ASN Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 81 PHE Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 78 ASP Chi-restraints excluded: chain a residue 100 TYR Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain b residue 85 MET Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain d residue 66 PHE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 95 GLU Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain e residue 121 MET Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain f residue 75 GLU Chi-restraints excluded: chain g residue 56 LEU Chi-restraints excluded: chain g residue 59 LEU Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain h residue 63 MET Chi-restraints excluded: chain h residue 95 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 191 optimal weight: 0.9990 chunk 513 optimal weight: 50.0000 chunk 112 optimal weight: 20.0000 chunk 334 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 570 optimal weight: 10.0000 chunk 473 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 188 optimal weight: 0.7980 chunk 299 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN C 177 ASN C 190 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 55165 Z= 0.230 Angle : 0.560 10.326 76198 Z= 0.320 Chirality : 0.041 0.158 8547 Planarity : 0.004 0.053 8448 Dihedral : 22.364 94.986 10519 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.25 % Allowed : 10.10 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % 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: 0.39 (0.11), residues: 5591 helix: 1.26 (0.11), residues: 2332 sheet: -0.36 (0.17), residues: 850 loop : -0.40 (0.13), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 453 HIS 0.011 0.001 HIS I 100 PHE 0.018 0.001 PHE C 184 TYR 0.016 0.001 TYR C 208 ARG 0.007 0.000 ARG B 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 33 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Evaluate side-chains 354 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 292 time to evaluate : 6.034 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: -0.1908 (mtp) cc_final: -0.2468 (ppp) REVERT: A 769 MET cc_start: 0.8543 (mtm) cc_final: 0.8338 (mtm) REVERT: B 93 LEU cc_start: 0.8929 (tp) cc_final: 0.8549 (tt) REVERT: B 901 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8868 (p) REVERT: B 1165 MET cc_start: 0.9060 (tpp) cc_final: 0.8615 (tpp) REVERT: C 66 HIS cc_start: 0.8794 (OUTLIER) cc_final: 0.8456 (t70) REVERT: E 91 CYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7836 (p) REVERT: F 127 ASP cc_start: 0.6325 (p0) cc_final: 0.6020 (p0) REVERT: G 7 LEU cc_start: 0.8796 (mt) cc_final: 0.8553 (mp) REVERT: G 104 MET cc_start: 0.4001 (tmm) cc_final: 0.3650 (tmm) REVERT: H 145 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.6302 (mpp) REVERT: V 1 MET cc_start: 0.2170 (ptm) cc_final: 0.1167 (mmt) outliers start: 62 outliers final: 52 residues processed: 336 average time/residue: 1.2285 time to fit residues: 702.0445 Evaluate side-chains 338 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 282 time to evaluate : 5.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 968 ASN Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 32 MET Chi-restraints excluded: chain M residue 129 ASN Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 81 PHE Chi-restraints excluded: chain a residue 100 TYR Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain c residue 59 LEU Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain d residue 66 PHE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain e residue 95 GLU Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain f residue 75 GLU Chi-restraints excluded: chain g residue 56 LEU Chi-restraints excluded: chain g residue 59 LEU Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain h residue 81 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 550 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 325 optimal weight: 6.9990 chunk 416 optimal weight: 10.0000 chunk 322 optimal weight: 6.9990 chunk 480 optimal weight: 20.0000 chunk 318 optimal weight: 1.9990 chunk 568 optimal weight: 10.0000 chunk 355 optimal weight: 30.0000 chunk 346 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 55165 Z= 0.285 Angle : 0.568 10.664 76198 Z= 0.325 Chirality : 0.041 0.187 8547 Planarity : 0.004 0.056 8448 Dihedral : 22.338 95.392 10519 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.43 % Allowed : 10.26 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % 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: 0.41 (0.11), residues: 5591 helix: 1.29 (0.11), residues: 2339 sheet: -0.35 (0.17), residues: 871 loop : -0.42 (0.13), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 453 HIS 0.010 0.001 HIS I 100 PHE 0.033 0.001 PHE C 38 TYR 0.036 0.002 TYR C 208 ARG 0.004 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 33 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Evaluate side-chains 352 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 281 time to evaluate : 6.216 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: -0.1899 (mtp) cc_final: -0.2486 (ppp) REVERT: A 769 MET cc_start: 0.8527 (mtm) cc_final: 0.8318 (mtm) REVERT: B 93 LEU cc_start: 0.8967 (tp) cc_final: 0.8585 (tt) REVERT: B 176 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: B 1165 MET cc_start: 0.9078 (tpp) cc_final: 0.8613 (tpp) REVERT: C 66 HIS cc_start: 0.8807 (OUTLIER) cc_final: 0.8471 (t70) REVERT: E 91 CYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8039 (p) REVERT: F 127 ASP cc_start: 0.6356 (p0) cc_final: 0.6020 (p0) REVERT: G 7 LEU cc_start: 0.8868 (mt) cc_final: 0.8628 (mp) REVERT: G 104 MET cc_start: 0.4070 (tmm) cc_final: 0.3737 (tmm) REVERT: V 1 MET cc_start: 0.2170 (ptm) cc_final: 0.1172 (mmt) outliers start: 71 outliers final: 57 residues processed: 333 average time/residue: 1.2192 time to fit residues: 692.1210 Evaluate side-chains 338 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 278 time to evaluate : 5.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 968 ASN Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 129 ASN Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 81 PHE Chi-restraints excluded: chain a residue 100 TYR Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain c residue 59 LEU Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain d residue 66 PHE Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain e residue 95 GLU Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain f residue 75 GLU Chi-restraints excluded: chain g residue 56 LEU Chi-restraints excluded: chain g residue 59 LEU Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain h residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 351 optimal weight: 30.0000 chunk 227 optimal weight: 10.0000 chunk 339 optimal weight: 7.9990 chunk 171 optimal weight: 30.0000 chunk 111 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 361 optimal weight: 6.9990 chunk 387 optimal weight: 9.9990 chunk 281 optimal weight: 30.0000 chunk 52 optimal weight: 0.9980 chunk 446 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN A1042 ASN ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 GLN D 102 ASN E 148 HIS ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 55165 Z= 0.485 Angle : 0.674 8.635 76198 Z= 0.386 Chirality : 0.045 0.203 8547 Planarity : 0.005 0.063 8448 Dihedral : 22.535 96.966 10519 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.77 % Allowed : 10.68 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % 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: -0.26 (0.11), residues: 5591 helix: 0.71 (0.11), residues: 2326 sheet: -0.61 (0.17), residues: 813 loop : -0.79 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 506 HIS 0.011 0.002 HIS A 84 PHE 0.026 0.002 PHE K 105 TYR 0.038 0.002 TYR B 388 ARG 0.008 0.001 ARG A 880 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 33 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Evaluate side-chains 356 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 268 time to evaluate : 6.027 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7024 (ppt170) REVERT: A 266 MET cc_start: -0.1807 (mtp) cc_final: -0.2398 (ppp) REVERT: A 769 MET cc_start: 0.8496 (mtm) cc_final: 0.8269 (mtm) REVERT: B 93 LEU cc_start: 0.9025 (tp) cc_final: 0.8663 (tt) REVERT: B 176 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: B 675 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7947 (tt) REVERT: B 1165 MET cc_start: 0.9108 (tpp) cc_final: 0.8633 (tpp) REVERT: C 61 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: C 66 HIS cc_start: 0.8932 (OUTLIER) cc_final: 0.8566 (t70) REVERT: F 127 ASP cc_start: 0.6440 (p0) cc_final: 0.6069 (p0) REVERT: G 7 LEU cc_start: 0.8904 (mt) cc_final: 0.8683 (mp) REVERT: G 104 MET cc_start: 0.4314 (tmm) cc_final: 0.3958 (tmm) REVERT: H 145 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6144 (mpp) REVERT: O 202 MET cc_start: 0.9043 (mtp) cc_final: 0.8809 (mtp) REVERT: V 1 MET cc_start: 0.2359 (ptm) cc_final: 0.1273 (mmt) outliers start: 88 outliers final: 69 residues processed: 333 average time/residue: 1.2141 time to fit residues: 690.7528 Evaluate side-chains 337 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 262 time to evaluate : 5.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 1030 ASN Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1145 GLN Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 17 CYS Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 129 ASN Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 81 PHE Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 100 TYR Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 106 GLU Chi-restraints excluded: chain b residue 62 PHE Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain d residue 66 PHE Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain e residue 95 GLU Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain f residue 75 GLU Chi-restraints excluded: chain f residue 86 ASP Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain h residue 81 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 517 optimal weight: 20.0000 chunk 544 optimal weight: 20.0000 chunk 497 optimal weight: 10.0000 chunk 529 optimal weight: 30.0000 chunk 318 optimal weight: 1.9990 chunk 230 optimal weight: 0.5980 chunk 416 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 478 optimal weight: 40.0000 chunk 501 optimal weight: 40.0000 chunk 528 optimal weight: 5.9990 overall best weight: 5.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 HIS E 95 GLN ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 55165 Z= 0.372 Angle : 0.613 9.588 76198 Z= 0.351 Chirality : 0.043 0.191 8547 Planarity : 0.005 0.060 8448 Dihedral : 22.605 98.816 10519 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.43 % Allowed : 11.21 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % 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: -0.17 (0.11), residues: 5591 helix: 0.84 (0.11), residues: 2333 sheet: -0.62 (0.17), residues: 816 loop : -0.78 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 453 HIS 0.011 0.001 HIS A 84 PHE 0.021 0.002 PHE C 184 TYR 0.020 0.002 TYR C 208 ARG 0.011 0.001 ARG e 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 33 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 266 time to evaluate : 5.768 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: -0.1789 (mtp) cc_final: -0.2395 (ppp) REVERT: A 769 MET cc_start: 0.8502 (mtm) cc_final: 0.8293 (mtm) REVERT: B 93 LEU cc_start: 0.8994 (tp) cc_final: 0.8611 (tt) REVERT: B 176 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7167 (tt0) REVERT: B 1165 MET cc_start: 0.9128 (tpp) cc_final: 0.8598 (tpp) REVERT: C 66 HIS cc_start: 0.8920 (OUTLIER) cc_final: 0.8532 (t70) REVERT: F 127 ASP cc_start: 0.6425 (p0) cc_final: 0.6027 (p0) REVERT: G 7 LEU cc_start: 0.8905 (mt) cc_final: 0.8688 (mp) REVERT: G 104 MET cc_start: 0.4263 (tmm) cc_final: 0.3865 (tmm) REVERT: O 202 MET cc_start: 0.9024 (mtp) cc_final: 0.8791 (mtp) REVERT: V 1 MET cc_start: 0.2464 (ptm) cc_final: 0.1320 (mmt) outliers start: 71 outliers final: 63 residues processed: 318 average time/residue: 1.1924 time to fit residues: 651.8295 Evaluate side-chains 326 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 261 time to evaluate : 5.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1017 ASP Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1145 GLN Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 17 CYS Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 129 ASN Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 81 PHE Chi-restraints excluded: chain a residue 78 ASP Chi-restraints excluded: chain a residue 100 TYR Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain d residue 66 PHE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain e residue 95 GLU Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain f residue 75 GLU Chi-restraints excluded: chain f residue 86 ASP Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain h residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 347 optimal weight: 0.1980 chunk 560 optimal weight: 10.0000 chunk 342 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 389 optimal weight: 0.9980 chunk 587 optimal weight: 0.9990 chunk 540 optimal weight: 7.9990 chunk 468 optimal weight: 6.9990 chunk 48 optimal weight: 0.0770 chunk 361 optimal weight: 5.9990 chunk 287 optimal weight: 0.2980 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1291 ASN ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 GLN M 129 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 55165 Z= 0.170 Angle : 0.552 12.409 76198 Z= 0.309 Chirality : 0.041 0.166 8547 Planarity : 0.004 0.090 8448 Dihedral : 22.450 100.057 10519 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.89 % Allowed : 11.75 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % 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: 0.61 (0.11), residues: 5591 helix: 1.53 (0.11), residues: 2325 sheet: -0.40 (0.17), residues: 847 loop : -0.33 (0.13), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 453 HIS 0.011 0.001 HIS I 100 PHE 0.019 0.001 PHE A 548 TYR 0.019 0.001 TYR C 208 ARG 0.007 0.001 ARG h 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 33 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Evaluate side-chains 324 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 280 time to evaluate : 5.803 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: -0.1774 (mtp) cc_final: -0.2466 (ppp) REVERT: A 1451 MET cc_start: 0.3652 (tmm) cc_final: 0.2926 (tmm) REVERT: B 93 LEU cc_start: 0.8875 (tp) cc_final: 0.8508 (tt) REVERT: B 1165 MET cc_start: 0.9101 (tpp) cc_final: 0.8541 (tpp) REVERT: C 66 HIS cc_start: 0.8743 (OUTLIER) cc_final: 0.8449 (t70) REVERT: F 127 ASP cc_start: 0.6099 (p0) cc_final: 0.5693 (p0) REVERT: G 104 MET cc_start: 0.4242 (tmm) cc_final: 0.3848 (tmm) REVERT: V 1 MET cc_start: 0.2301 (ptm) cc_final: 0.1128 (mmt) outliers start: 44 outliers final: 40 residues processed: 310 average time/residue: 1.1833 time to fit residues: 625.5973 Evaluate side-chains 315 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 274 time to evaluate : 5.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 968 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 17 CYS Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain M residue 129 ASN Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 81 PHE Chi-restraints excluded: chain a residue 100 TYR Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain d residue 66 PHE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain e residue 95 GLU Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain g residue 56 LEU Chi-restraints excluded: chain h residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 371 optimal weight: 5.9990 chunk 498 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 431 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 468 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 481 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.079931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.062813 restraints weight = 975516.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.062695 restraints weight = 742764.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.063165 restraints weight = 473885.877| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 55165 Z= 0.242 Angle : 0.551 10.573 76198 Z= 0.313 Chirality : 0.041 0.181 8547 Planarity : 0.004 0.054 8448 Dihedral : 22.388 100.707 10519 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.89 % Allowed : 11.79 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.21 % 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: 0.57 (0.11), residues: 5591 helix: 1.52 (0.11), residues: 2330 sheet: -0.44 (0.17), residues: 860 loop : -0.37 (0.13), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 99 HIS 0.010 0.001 HIS I 100 PHE 0.018 0.001 PHE C 184 TYR 0.014 0.001 TYR B1048 ARG 0.007 0.000 ARG e 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16983.45 seconds wall clock time: 297 minutes 13.32 seconds (17833.32 seconds total)