Starting phenix.real_space_refine on Sun Mar 17 04:59:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxx_42788/03_2024/8uxx_42788_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxx_42788/03_2024/8uxx_42788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxx_42788/03_2024/8uxx_42788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxx_42788/03_2024/8uxx_42788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxx_42788/03_2024/8uxx_42788_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxx_42788/03_2024/8uxx_42788_trim_updated.pdb" } resolution = 3.2 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= 0.005 sd= 0.077 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: 9 Type Number sf(0) Gaussians P 21 5.49 5 Mg 10 5.21 5 S 230 5.16 5 Be 7 3.05 5 C 24684 2.51 5 N 6643 2.21 5 O 7446 1.98 5 F 21 1.80 5 H 38268 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 139": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 227": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 239": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 257": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 264": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 286": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 348": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 352": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 360": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 383": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 418": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 419": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 26": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 99": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 187": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 195": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 238": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 295": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 324": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 380": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 85": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 122": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 178": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 255": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 288": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 321": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 325": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 351": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 371": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 125": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 227": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 248": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 255": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 266": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 285": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 297": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 144": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 167": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 71": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 144": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 77330 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 6226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 6226 Classifications: {'peptide': 400} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 379} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 6153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6153 Classifications: {'peptide': 387} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 367} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5576 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 340} Chain breaks: 1 Chain: "D" Number of atoms: 5153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 5153 Classifications: {'peptide': 316} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 300} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 160} Chain breaks: 1 Chain: "F" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2781 Classifications: {'peptide': 168} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "G" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 2362 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "H" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 5749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5749 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 15 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 26.40, per 1000 atoms: 0.34 Number of scatterers: 77330 At special positions: 0 Unit cell: (133.254, 204.592, 228.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) S 230 16.00 P 21 15.00 Mg 10 11.99 F 21 9.00 O 7446 8.00 N 6643 7.00 C 24684 6.00 Be 7 4.00 H 38268 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 217 " - pdb=" SG CYS N 257 " distance=2.08 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 50.18 Conformation dependent library (CDL) restraints added in 6.2 seconds 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9168 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 229 helices and 51 sheets defined 41.9% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.87 Creating SS restraints... Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.661A pdb=" N LEU A 81 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 114 Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 160 through 167 removed outlier: 3.586A pdb=" N LEU A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 213 through 226 Processing helix chain 'A' and resid 234 through 244 removed outlier: 3.811A pdb=" N GLU A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.766A pdb=" N LEU A 288 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 320 through 328 removed outlier: 4.621A pdb=" N LYS A 324 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 327 " --> pdb=" O LYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 342 through 365 Processing helix chain 'A' and resid 382 through 394 removed outlier: 3.789A pdb=" N ALA A 385 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 386 " --> pdb=" O ARG A 383 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 391 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 4.256A pdb=" N GLY A 400 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.676A pdb=" N GLN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 144 removed outlier: 3.506A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 196 removed outlier: 3.698A pdb=" N ARG B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.697A pdb=" N PHE B 206 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 214 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 216 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.764A pdb=" N ALA B 284 " --> pdb=" O ASP B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 removed outlier: 4.050A pdb=" N ALA B 296 " --> pdb=" O TYR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 324 removed outlier: 3.698A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 323 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 Proline residue: B 334 - end of helix Processing helix chain 'B' and resid 346 through 360 removed outlier: 5.043A pdb=" N VAL B 350 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 352 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 355 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA B 358 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 384 removed outlier: 3.933A pdb=" N GLU B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N VAL B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ARG B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LYS B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 295 Processing helix chain 'C' and resid 317 through 329 Processing helix chain 'D' and resid 9 through 20 removed outlier: 3.558A pdb=" N SER D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 59 through 64 removed outlier: 3.723A pdb=" N ASN D 64 " --> pdb=" O PRO D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 78 removed outlier: 7.332A pdb=" N ALA D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 121 through 139 removed outlier: 3.558A pdb=" N ASP D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 154 removed outlier: 3.714A pdb=" N SER D 153 " --> pdb=" O LYS D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 203 removed outlier: 4.003A pdb=" N VAL D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 255 through 263 Processing helix chain 'D' and resid 265 through 298 removed outlier: 3.659A pdb=" N GLN D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 286 " --> pdb=" O GLN D 282 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 10 Processing helix chain 'E' and resid 43 through 54 removed outlier: 4.516A pdb=" N ARG E 52 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA E 53 " --> pdb=" O GLY E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 83 removed outlier: 3.722A pdb=" N SER E 78 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 101 removed outlier: 4.378A pdb=" N ARG E 94 " --> pdb=" O ARG E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 149 removed outlier: 3.575A pdb=" N SER E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS E 148 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 166 removed outlier: 5.590A pdb=" N PHE E 164 " --> pdb=" O TRP E 160 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER E 165 " --> pdb=" O TRP E 161 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LYS E 166 " --> pdb=" O THR E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 171 No H-bonds generated for 'chain 'E' and resid 169 through 171' Processing helix chain 'F' and resid 6 through 19 Processing helix chain 'F' and resid 37 through 40 No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 44 through 46 No H-bonds generated for 'chain 'F' and resid 44 through 46' Processing helix chain 'F' and resid 81 through 96 removed outlier: 3.571A pdb=" N GLN F 92 " --> pdb=" O ARG F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 128 through 167 removed outlier: 4.824A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS F 167 " --> pdb=" O THR F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 5 No H-bonds generated for 'chain 'G' and resid 3 through 5' Processing helix chain 'G' and resid 9 through 12 No H-bonds generated for 'chain 'G' and resid 9 through 12' Processing helix chain 'G' and resid 18 through 21 No H-bonds generated for 'chain 'G' and resid 18 through 21' Processing helix chain 'G' and resid 29 through 48 removed outlier: 3.691A pdb=" N LEU G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Proline residue: G 41 - end of helix Processing helix chain 'G' and resid 52 through 61 removed outlier: 3.764A pdb=" N SER G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 86 removed outlier: 4.393A pdb=" N GLN G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 98 removed outlier: 4.125A pdb=" N GLU G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 114 removed outlier: 3.817A pdb=" N ASN G 109 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG G 113 " --> pdb=" O ASN G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 137 Processing helix chain 'G' and resid 139 through 146 removed outlier: 3.962A pdb=" N ARG G 144 " --> pdb=" O CYS G 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 removed outlier: 3.586A pdb=" N GLN H 59 " --> pdb=" O ASP H 56 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER H 60 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 79 through 91 removed outlier: 4.393A pdb=" N LYS H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 137 through 145 removed outlier: 3.816A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 196 removed outlier: 4.055A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 216 Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 234 through 236 No H-bonds generated for 'chain 'H' and resid 234 through 236' Processing helix chain 'H' and resid 252 through 261 removed outlier: 3.932A pdb=" N ARG H 256 " --> pdb=" O GLU H 253 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N CYS H 257 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 264 through 267 Processing helix chain 'H' and resid 274 through 284 Processing helix chain 'H' and resid 287 through 295 removed outlier: 3.855A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR H 294 " --> pdb=" O ARG H 290 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA H 295 " --> pdb=" O LYS H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 305 Processing helix chain 'H' and resid 309 through 320 removed outlier: 3.669A pdb=" N ALA H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU H 320 " --> pdb=" O GLU H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 348 removed outlier: 5.382A pdb=" N VAL H 339 " --> pdb=" O LYS H 336 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY H 342 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA H 347 " --> pdb=" O SER H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 352 No H-bonds generated for 'chain 'H' and resid 350 through 352' Processing helix chain 'H' and resid 359 through 363 Processing helix chain 'H' and resid 367 through 373 removed outlier: 3.565A pdb=" N HIS H 371 " --> pdb=" O SER H 368 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS H 373 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 64 removed outlier: 5.888A pdb=" N GLY I 63 " --> pdb=" O GLN I 59 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE I 64 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 91 removed outlier: 4.277A pdb=" N LYS I 84 " --> pdb=" O ASP I 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS I 87 " --> pdb=" O GLU I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'I' and resid 113 through 125 removed outlier: 3.604A pdb=" N GLU I 117 " --> pdb=" O LYS I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 142 Processing helix chain 'I' and resid 182 through 196 removed outlier: 3.698A pdb=" N THR I 194 " --> pdb=" O MET I 190 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU I 195 " --> pdb=" O LYS I 191 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG I 196 " --> pdb=" O ILE I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 216 removed outlier: 3.840A pdb=" N GLU I 207 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 232 removed outlier: 3.851A pdb=" N ALA I 228 " --> pdb=" O GLU I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 236 No H-bonds generated for 'chain 'I' and resid 234 through 236' Processing helix chain 'I' and resid 252 through 262 removed outlier: 3.636A pdb=" N ARG I 256 " --> pdb=" O GLU I 253 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N CYS I 257 " --> pdb=" O ARG I 254 " (cutoff:3.500A) Proline residue: I 258 - end of helix Processing helix chain 'I' and resid 264 through 267 Processing helix chain 'I' and resid 274 through 284 removed outlier: 3.547A pdb=" N THR I 278 " --> pdb=" O ILE I 274 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS I 284 " --> pdb=" O ASN I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 295 removed outlier: 3.839A pdb=" N LEU I 293 " --> pdb=" O ARG I 290 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TYR I 294 " --> pdb=" O LYS I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 305 Processing helix chain 'I' and resid 309 through 320 Processing helix chain 'I' and resid 335 through 348 removed outlier: 5.721A pdb=" N VAL I 339 " --> pdb=" O LYS I 336 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY I 342 " --> pdb=" O VAL I 339 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA I 347 " --> pdb=" O SER I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 352 through 354 No H-bonds generated for 'chain 'I' and resid 352 through 354' Processing helix chain 'I' and resid 359 through 373 removed outlier: 4.839A pdb=" N GLU I 364 " --> pdb=" O GLN I 360 " (cutoff:3.500A) Proline residue: I 367 - end of helix removed outlier: 5.478A pdb=" N VAL I 370 " --> pdb=" O GLY I 366 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N HIS I 371 " --> pdb=" O PRO I 367 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ARG I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS I 373 " --> pdb=" O ILE I 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 60 Processing helix chain 'M' and resid 62 through 64 No H-bonds generated for 'chain 'M' and resid 62 through 64' Processing helix chain 'M' and resid 79 through 91 Processing helix chain 'M' and resid 98 through 100 No H-bonds generated for 'chain 'M' and resid 98 through 100' Processing helix chain 'M' and resid 113 through 125 removed outlier: 3.560A pdb=" N MET M 123 " --> pdb=" O MET M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 145 removed outlier: 3.771A pdb=" N SER M 141 " --> pdb=" O GLN M 137 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU M 142 " --> pdb=" O ALA M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 196 removed outlier: 4.627A pdb=" N THR M 194 " --> pdb=" O MET M 190 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU M 195 " --> pdb=" O LYS M 191 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG M 196 " --> pdb=" O ILE M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 213 Processing helix chain 'M' and resid 223 through 230 Processing helix chain 'M' and resid 252 through 256 removed outlier: 3.648A pdb=" N ARG M 256 " --> pdb=" O GLU M 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 261 Processing helix chain 'M' and resid 264 through 267 Processing helix chain 'M' and resid 274 through 283 Processing helix chain 'M' and resid 289 through 294 removed outlier: 3.907A pdb=" N TYR M 294 " --> pdb=" O LYS M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 305 Processing helix chain 'M' and resid 309 through 320 Processing helix chain 'M' and resid 335 through 348 removed outlier: 5.343A pdb=" N VAL M 339 " --> pdb=" O LYS M 336 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE M 341 " --> pdb=" O SER M 338 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA M 347 " --> pdb=" O SER M 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 352 through 354 No H-bonds generated for 'chain 'M' and resid 352 through 354' Processing helix chain 'M' and resid 359 through 362 No H-bonds generated for 'chain 'M' and resid 359 through 362' Processing helix chain 'M' and resid 367 through 373 removed outlier: 3.531A pdb=" N HIS M 371 " --> pdb=" O SER M 368 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS M 373 " --> pdb=" O VAL M 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 64 removed outlier: 5.849A pdb=" N GLY N 63 " --> pdb=" O GLN N 59 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE N 64 " --> pdb=" O SER N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 91 removed outlier: 3.817A pdb=" N LYS N 84 " --> pdb=" O ASP N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 100 No H-bonds generated for 'chain 'N' and resid 98 through 100' Processing helix chain 'N' and resid 113 through 125 Processing helix chain 'N' and resid 137 through 144 removed outlier: 3.949A pdb=" N SER N 141 " --> pdb=" O GLN N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 182 through 196 removed outlier: 3.819A pdb=" N THR N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU N 195 " --> pdb=" O LYS N 191 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG N 196 " --> pdb=" O ILE N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 216 removed outlier: 4.205A pdb=" N LYS N 215 " --> pdb=" O ASP N 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 230 Processing helix chain 'N' and resid 252 through 261 removed outlier: 4.053A pdb=" N ARG N 256 " --> pdb=" O GLU N 253 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS N 257 " --> pdb=" O ARG N 254 " (cutoff:3.500A) Proline residue: N 258 - end of helix Processing helix chain 'N' and resid 264 through 267 Processing helix chain 'N' and resid 274 through 284 Processing helix chain 'N' and resid 290 through 295 Processing helix chain 'N' and resid 302 through 305 Processing helix chain 'N' and resid 309 through 320 Processing helix chain 'N' and resid 338 through 348 removed outlier: 3.869A pdb=" N SER N 348 " --> pdb=" O SER N 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 359 through 365 removed outlier: 3.783A pdb=" N GLU N 364 " --> pdb=" O GLN N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 367 through 374 removed outlier: 3.829A pdb=" N LYS N 373 " --> pdb=" O VAL N 370 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 64 removed outlier: 3.572A pdb=" N GLN O 59 " --> pdb=" O ASP O 56 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER O 60 " --> pdb=" O GLU O 57 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG O 62 " --> pdb=" O GLN O 59 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLY O 63 " --> pdb=" O SER O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 91 removed outlier: 3.886A pdb=" N LYS O 84 " --> pdb=" O ASP O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 100 No H-bonds generated for 'chain 'O' and resid 98 through 100' Processing helix chain 'O' and resid 113 through 125 removed outlier: 3.630A pdb=" N MET O 123 " --> pdb=" O MET O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 145 removed outlier: 3.998A pdb=" N LEU O 142 " --> pdb=" O ALA O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 174 No H-bonds generated for 'chain 'O' and resid 172 through 174' Processing helix chain 'O' and resid 182 through 196 removed outlier: 4.182A pdb=" N GLU O 195 " --> pdb=" O LYS O 191 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG O 196 " --> pdb=" O ILE O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 205 through 216 removed outlier: 4.153A pdb=" N LYS O 215 " --> pdb=" O ASP O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 230 removed outlier: 3.710A pdb=" N ALA O 228 " --> pdb=" O GLU O 224 " (cutoff:3.500A) Processing helix chain 'O' and resid 252 through 261 removed outlier: 3.777A pdb=" N ARG O 256 " --> pdb=" O GLU O 253 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N CYS O 257 " --> pdb=" O ARG O 254 " (cutoff:3.500A) Proline residue: O 258 - end of helix Processing helix chain 'O' and resid 264 through 267 Processing helix chain 'O' and resid 274 through 284 Processing helix chain 'O' and resid 287 through 296 removed outlier: 3.577A pdb=" N ARG O 290 " --> pdb=" O ILE O 287 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS O 291 " --> pdb=" O ASP O 288 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA O 295 " --> pdb=" O ASP O 292 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 305 Processing helix chain 'O' and resid 309 through 320 Processing helix chain 'O' and resid 333 through 348 removed outlier: 4.279A pdb=" N LYS O 336 " --> pdb=" O PRO O 333 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER O 338 " --> pdb=" O ARG O 335 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL O 339 " --> pdb=" O LYS O 336 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY O 342 " --> pdb=" O VAL O 339 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA O 347 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 352 through 354 No H-bonds generated for 'chain 'O' and resid 352 through 354' Processing helix chain 'O' and resid 359 through 365 Processing helix chain 'O' and resid 367 through 372 removed outlier: 3.660A pdb=" N VAL O 370 " --> pdb=" O PRO O 367 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 60 Processing helix chain 'P' and resid 62 through 64 No H-bonds generated for 'chain 'P' and resid 62 through 64' Processing helix chain 'P' and resid 79 through 91 removed outlier: 3.702A pdb=" N LYS P 84 " --> pdb=" O ASP P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 100 No H-bonds generated for 'chain 'P' and resid 98 through 100' Processing helix chain 'P' and resid 113 through 125 Processing helix chain 'P' and resid 137 through 145 removed outlier: 4.313A pdb=" N LEU P 142 " --> pdb=" O ALA P 138 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR P 143 " --> pdb=" O VAL P 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 174 No H-bonds generated for 'chain 'P' and resid 172 through 174' Processing helix chain 'P' and resid 182 through 196 removed outlier: 3.908A pdb=" N GLU P 195 " --> pdb=" O LYS P 191 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG P 196 " --> pdb=" O ILE P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 215 removed outlier: 3.713A pdb=" N GLU P 207 " --> pdb=" O THR P 203 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE P 208 " --> pdb=" O ALA P 204 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU P 214 " --> pdb=" O ARG P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 232 removed outlier: 3.515A pdb=" N SER P 232 " --> pdb=" O ALA P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 252 through 261 removed outlier: 4.177A pdb=" N ARG P 256 " --> pdb=" O GLU P 253 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS P 257 " --> pdb=" O ARG P 254 " (cutoff:3.500A) Proline residue: P 258 - end of helix Processing helix chain 'P' and resid 264 through 267 Processing helix chain 'P' and resid 274 through 284 Processing helix chain 'P' and resid 287 through 294 removed outlier: 4.417A pdb=" N LYS P 291 " --> pdb=" O ASP P 288 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR P 294 " --> pdb=" O LYS P 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 302 through 305 Processing helix chain 'P' and resid 309 through 320 Processing helix chain 'P' and resid 335 through 348 removed outlier: 5.380A pdb=" N VAL P 339 " --> pdb=" O LYS P 336 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY P 342 " --> pdb=" O VAL P 339 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA P 347 " --> pdb=" O SER P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 359 through 365 Processing helix chain 'P' and resid 367 through 369 No H-bonds generated for 'chain 'P' and resid 367 through 369' Processing helix chain 'Q' and resid 56 through 60 Processing helix chain 'Q' and resid 62 through 64 No H-bonds generated for 'chain 'Q' and resid 62 through 64' Processing helix chain 'Q' and resid 79 through 91 removed outlier: 3.547A pdb=" N ILE Q 85 " --> pdb=" O ASP Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 100 No H-bonds generated for 'chain 'Q' and resid 98 through 100' Processing helix chain 'Q' and resid 113 through 125 removed outlier: 3.511A pdb=" N MET Q 123 " --> pdb=" O MET Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 145 removed outlier: 3.612A pdb=" N LEU Q 142 " --> pdb=" O ALA Q 138 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR Q 143 " --> pdb=" O VAL Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 182 through 196 removed outlier: 3.632A pdb=" N THR Q 194 " --> pdb=" O MET Q 190 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU Q 195 " --> pdb=" O LYS Q 191 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG Q 196 " --> pdb=" O ILE Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 205 through 216 Processing helix chain 'Q' and resid 223 through 230 Processing helix chain 'Q' and resid 252 through 256 removed outlier: 3.968A pdb=" N ARG Q 256 " --> pdb=" O GLU Q 253 " (cutoff:3.500A) Processing helix chain 'Q' and resid 258 through 261 Processing helix chain 'Q' and resid 264 through 267 Processing helix chain 'Q' and resid 274 through 284 Processing helix chain 'Q' and resid 287 through 293 removed outlier: 4.433A pdb=" N LYS Q 291 " --> pdb=" O ILE Q 287 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP Q 292 " --> pdb=" O ASP Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 Processing helix chain 'Q' and resid 309 through 320 Processing helix chain 'Q' and resid 335 through 348 removed outlier: 5.681A pdb=" N VAL Q 339 " --> pdb=" O LYS Q 336 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE Q 341 " --> pdb=" O SER Q 338 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA Q 347 " --> pdb=" O SER Q 344 " (cutoff:3.500A) Processing helix chain 'Q' and resid 359 through 363 Processing helix chain 'Q' and resid 367 through 372 removed outlier: 3.814A pdb=" N HIS Q 371 " --> pdb=" O SER Q 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 60 Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'R' and resid 79 through 91 removed outlier: 3.965A pdb=" N LYS R 84 " --> pdb=" O ASP R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 125 Processing helix chain 'R' and resid 137 through 144 removed outlier: 4.085A pdb=" N SER R 141 " --> pdb=" O GLN R 137 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 174 No H-bonds generated for 'chain 'R' and resid 172 through 174' Processing helix chain 'R' and resid 182 through 196 removed outlier: 4.535A pdb=" N GLU R 195 " --> pdb=" O LYS R 191 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG R 196 " --> pdb=" O ILE R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 216 removed outlier: 3.704A pdb=" N GLU R 207 " --> pdb=" O THR R 203 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE R 208 " --> pdb=" O ALA R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 235 removed outlier: 4.013A pdb=" N ALA R 231 " --> pdb=" O MET R 227 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER R 233 " --> pdb=" O THR R 229 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N SER R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N SER R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 261 removed outlier: 3.978A pdb=" N ARG R 256 " --> pdb=" O GLU R 253 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N CYS R 257 " --> pdb=" O ARG R 254 " (cutoff:3.500A) Proline residue: R 258 - end of helix Processing helix chain 'R' and resid 264 through 267 Processing helix chain 'R' and resid 274 through 284 Processing helix chain 'R' and resid 290 through 296 Processing helix chain 'R' and resid 302 through 305 Processing helix chain 'R' and resid 309 through 320 removed outlier: 3.524A pdb=" N LEU R 320 " --> pdb=" O GLU R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 348 removed outlier: 5.212A pdb=" N VAL R 339 " --> pdb=" O LYS R 336 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA R 347 " --> pdb=" O SER R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 352 through 354 No H-bonds generated for 'chain 'R' and resid 352 through 354' Processing helix chain 'R' and resid 359 through 362 No H-bonds generated for 'chain 'R' and resid 359 through 362' Processing helix chain 'R' and resid 367 through 373 Processing sheet with id= A, first strand: chain 'A' and resid 154 through 159 removed outlier: 6.536A pdb=" N ILE A 8 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR A 129 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N MET A 10 " --> pdb=" O THR A 129 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 330 through 333 removed outlier: 6.580A pdb=" N THR A 182 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SER A 333 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 184 " --> pdb=" O SER A 333 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 131 through 136 removed outlier: 6.971A pdb=" N ILE B 6 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N THR B 106 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N LEU B 8 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 32 through 36 Processing sheet with id= F, first strand: chain 'B' and resid 298 through 300 Processing sheet with id= G, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= H, first strand: chain 'C' and resid 17 through 19 removed outlier: 3.601A pdb=" N ARG C 49 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU C 39 " --> pdb=" O HIS C 47 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N HIS C 47 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASP C 41 " --> pdb=" O TRP C 45 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TRP C 45 " --> pdb=" O ASP C 41 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 90 through 95 removed outlier: 3.837A pdb=" N ALA C 79 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS C 60 " --> pdb=" O CYS C 73 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 135 through 141 removed outlier: 3.768A pdb=" N TRP C 135 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE C 105 " --> pdb=" O GLY C 118 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 149 through 154 removed outlier: 6.661A pdb=" N GLY C 164 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU C 152 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA C 162 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TRP C 154 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU C 160 " --> pdb=" O TRP C 154 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 169 " --> pdb=" O CYS C 165 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 200 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER C 174 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL C 198 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 243 through 248 removed outlier: 3.683A pdb=" N ALA C 243 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 210 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 254 through 259 removed outlier: 6.820A pdb=" N ALA C 268 " --> pdb=" O ARG C 255 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU C 257 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL C 266 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TRP C 259 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA C 264 " --> pdb=" O TRP C 259 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLN C 278 " --> pdb=" O HIS C 286 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N HIS C 286 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASN C 280 " --> pdb=" O TRP C 284 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TRP C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 3 through 9 removed outlier: 6.776A pdb=" N VAL C 372 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 28 through 32 Processing sheet with id= P, first strand: chain 'D' and resid 157 through 159 Processing sheet with id= Q, first strand: chain 'F' and resid 51 through 54 Processing sheet with id= R, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.770A pdb=" N THR H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ALA H 135 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 35 through 38 Processing sheet with id= T, first strand: chain 'H' and resid 149 through 155 removed outlier: 3.515A pdb=" N VAL H 152 " --> pdb=" O VAL H 163 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 238 through 241 Processing sheet with id= V, first strand: chain 'I' and resid 29 through 32 removed outlier: 8.170A pdb=" N CYS I 10 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU I 104 " --> pdb=" O CYS I 10 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 35 through 38 Processing sheet with id= X, first strand: chain 'I' and resid 150 through 155 Processing sheet with id= Y, first strand: chain 'I' and resid 238 through 241 Processing sheet with id= Z, first strand: chain 'M' and resid 132 through 136 removed outlier: 6.602A pdb=" N THR M 103 " --> pdb=" O TYR M 133 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA M 135 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU M 105 " --> pdb=" O ALA M 135 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU M 8 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR M 106 " --> pdb=" O LEU M 8 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N CYS M 10 " --> pdb=" O THR M 106 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 35 through 38 Processing sheet with id= AB, first strand: chain 'M' and resid 297 through 300 removed outlier: 6.455A pdb=" N ILE M 151 " --> pdb=" O VAL M 298 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER M 300 " --> pdb=" O ILE M 151 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU M 153 " --> pdb=" O SER M 300 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'M' and resid 238 through 241 Processing sheet with id= AD, first strand: chain 'N' and resid 132 through 136 removed outlier: 6.875A pdb=" N THR N 103 " --> pdb=" O TYR N 133 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA N 135 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU N 105 " --> pdb=" O ALA N 135 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU N 8 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N THR N 106 " --> pdb=" O LEU N 8 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N CYS N 10 " --> pdb=" O THR N 106 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 35 through 38 Processing sheet with id= AF, first strand: chain 'N' and resid 297 through 300 removed outlier: 6.260A pdb=" N ILE N 151 " --> pdb=" O VAL N 298 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N SER N 300 " --> pdb=" O ILE N 151 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU N 153 " --> pdb=" O SER N 300 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 238 through 241 Processing sheet with id= AH, first strand: chain 'O' and resid 132 through 136 removed outlier: 6.592A pdb=" N THR O 103 " --> pdb=" O TYR O 133 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA O 135 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU O 105 " --> pdb=" O ALA O 135 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU O 8 " --> pdb=" O LEU O 104 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR O 106 " --> pdb=" O LEU O 8 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N CYS O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'O' and resid 35 through 38 removed outlier: 3.572A pdb=" N ARG O 37 " --> pdb=" O THR O 66 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'O' and resid 297 through 300 removed outlier: 6.288A pdb=" N ILE O 151 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER O 300 " --> pdb=" O ILE O 151 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU O 153 " --> pdb=" O SER O 300 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'O' and resid 238 through 241 Processing sheet with id= AL, first strand: chain 'P' and resid 132 through 136 removed outlier: 6.749A pdb=" N THR P 103 " --> pdb=" O TYR P 133 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA P 135 " --> pdb=" O THR P 103 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU P 105 " --> pdb=" O ALA P 135 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU P 8 " --> pdb=" O LEU P 104 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR P 106 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N CYS P 10 " --> pdb=" O THR P 106 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'P' and resid 35 through 38 removed outlier: 3.527A pdb=" N ARG P 37 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'P' and resid 297 through 300 removed outlier: 6.024A pdb=" N ILE P 151 " --> pdb=" O VAL P 298 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER P 300 " --> pdb=" O ILE P 151 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU P 153 " --> pdb=" O SER P 300 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'P' and resid 238 through 241 Processing sheet with id= AP, first strand: chain 'Q' and resid 8 through 12 Processing sheet with id= AQ, first strand: chain 'Q' and resid 34 through 38 Processing sheet with id= AR, first strand: chain 'Q' and resid 103 through 107 Processing sheet with id= AS, first strand: chain 'Q' and resid 297 through 300 removed outlier: 6.247A pdb=" N ILE Q 151 " --> pdb=" O VAL Q 298 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N SER Q 300 " --> pdb=" O ILE Q 151 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU Q 153 " --> pdb=" O SER Q 300 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL Q 163 " --> pdb=" O VAL Q 152 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 238 through 241 Processing sheet with id= AU, first strand: chain 'R' and resid 8 through 11 Processing sheet with id= AV, first strand: chain 'R' and resid 35 through 38 Processing sheet with id= AW, first strand: chain 'R' and resid 103 through 107 Processing sheet with id= AX, first strand: chain 'R' and resid 297 through 300 removed outlier: 6.470A pdb=" N ILE R 151 " --> pdb=" O VAL R 298 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER R 300 " --> pdb=" O ILE R 151 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU R 153 " --> pdb=" O SER R 300 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL R 163 " --> pdb=" O VAL R 152 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'R' and resid 238 through 241 1410 hydrogen bonds defined for protein. 3531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 27.80 Time building geometry restraints manager: 52.82 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: 38205 1.13 - 1.30: 7043 1.30 - 1.48: 15449 1.48 - 1.65: 17092 1.65 - 1.83: 395 Bond restraints: 78184 Sorted by residual: bond pdb=" N HIS H 101 " pdb=" H HIS H 101 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N THR Q 77 " pdb=" H THR Q 77 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N SER M 141 " pdb=" H SER M 141 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE2 GLN C 131 " pdb="HE22 GLN C 131 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CZ PHE Q 90 " pdb=" HZ PHE Q 90 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 78179 not shown) Histogram of bond angle deviations from ideal: 94.59 - 102.69: 379 102.69 - 110.78: 77661 110.78 - 118.88: 30791 118.88 - 126.98: 31753 126.98 - 135.08: 568 Bond angle restraints: 141152 Sorted by residual: angle pdb=" PA ATP B 902 " pdb=" O3A ATP B 902 " pdb=" PB ATP B 902 " ideal model delta sigma weight residual 136.83 119.58 17.25 1.00e+00 1.00e+00 2.98e+02 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 123.50 16.37 1.00e+00 1.00e+00 2.68e+02 angle pdb=" F2 BEF Q 403 " pdb=" BE BEF Q 403 " pdb=" F3 BEF Q 403 " ideal model delta sigma weight residual 119.96 96.45 23.51 3.00e+00 1.11e-01 6.14e+01 angle pdb=" O1B ADP H 802 " pdb=" PB ADP H 802 " pdb=" O3B ADP H 802 " ideal model delta sigma weight residual 119.90 97.31 22.59 3.00e+00 1.11e-01 5.67e+01 angle pdb=" O2B ADP M 401 " pdb=" PB ADP M 401 " pdb=" O3B ADP M 401 " ideal model delta sigma weight residual 119.90 98.13 21.77 3.00e+00 1.11e-01 5.27e+01 ... (remaining 141147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.92: 35099 30.92 - 61.84: 1551 61.84 - 92.76: 247 92.76 - 123.68: 10 123.68 - 154.60: 9 Dihedral angle restraints: 36916 sinusoidal: 20203 harmonic: 16713 Sorted by residual: dihedral pdb=" O1B ADP M 401 " pdb=" O3A ADP M 401 " pdb=" PB ADP M 401 " pdb=" PA ADP M 401 " ideal model delta sinusoidal sigma weight residual -60.00 94.60 -154.60 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" O2A ADP Q 401 " pdb=" O3A ADP Q 401 " pdb=" PA ADP Q 401 " pdb=" PB ADP Q 401 " ideal model delta sinusoidal sigma weight residual -60.00 87.97 -147.97 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O2A ADP O 401 " pdb=" O3A ADP O 401 " pdb=" PA ADP O 401 " pdb=" PB ADP O 401 " ideal model delta sinusoidal sigma weight residual -60.00 87.05 -147.05 1 2.00e+01 2.50e-03 4.41e+01 ... (remaining 36913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4097 0.101 - 0.201: 1593 0.201 - 0.302: 267 0.302 - 0.403: 29 0.403 - 0.504: 4 Chirality restraints: 5990 Sorted by residual: chirality pdb=" CA ARG Q 95 " pdb=" N ARG Q 95 " pdb=" C ARG Q 95 " pdb=" CB ARG Q 95 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" CA LYS F 150 " pdb=" N LYS F 150 " pdb=" C LYS F 150 " pdb=" CB LYS F 150 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA LYS F 128 " pdb=" N LYS F 128 " pdb=" C LYS F 128 " pdb=" CB LYS F 128 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 5987 not shown) Planarity restraints: 11601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 340 " -0.402 2.00e-02 2.50e+03 1.50e-01 9.01e+02 pdb=" CG TRP M 340 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP M 340 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TRP M 340 " 0.119 2.00e-02 2.50e+03 pdb=" NE1 TRP M 340 " 0.162 2.00e-02 2.50e+03 pdb=" CE2 TRP M 340 " 0.097 2.00e-02 2.50e+03 pdb=" CE3 TRP M 340 " 0.145 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 340 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 340 " 0.050 2.00e-02 2.50e+03 pdb=" CH2 TRP M 340 " -0.070 2.00e-02 2.50e+03 pdb=" HD1 TRP M 340 " -0.076 2.00e-02 2.50e+03 pdb=" HE1 TRP M 340 " 0.106 2.00e-02 2.50e+03 pdb=" HE3 TRP M 340 " 0.183 2.00e-02 2.50e+03 pdb=" HZ2 TRP M 340 " -0.123 2.00e-02 2.50e+03 pdb=" HZ3 TRP M 340 " 0.016 2.00e-02 2.50e+03 pdb=" HH2 TRP M 340 " -0.225 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 340 " -0.288 2.00e-02 2.50e+03 1.05e-01 4.40e+02 pdb=" CG TRP H 340 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP H 340 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP H 340 " 0.081 2.00e-02 2.50e+03 pdb=" NE1 TRP H 340 " 0.122 2.00e-02 2.50e+03 pdb=" CE2 TRP H 340 " 0.067 2.00e-02 2.50e+03 pdb=" CE3 TRP H 340 " 0.086 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 340 " -0.029 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 340 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP H 340 " -0.041 2.00e-02 2.50e+03 pdb=" HD1 TRP H 340 " -0.046 2.00e-02 2.50e+03 pdb=" HE1 TRP H 340 " 0.082 2.00e-02 2.50e+03 pdb=" HE3 TRP H 340 " 0.113 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 340 " -0.134 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 340 " 0.019 2.00e-02 2.50e+03 pdb=" HH2 TRP H 340 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 340 " -0.282 2.00e-02 2.50e+03 1.03e-01 4.21e+02 pdb=" CG TRP R 340 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP R 340 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP R 340 " 0.076 2.00e-02 2.50e+03 pdb=" NE1 TRP R 340 " 0.107 2.00e-02 2.50e+03 pdb=" CE2 TRP R 340 " 0.055 2.00e-02 2.50e+03 pdb=" CE3 TRP R 340 " 0.091 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 340 " -0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 340 " 0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP R 340 " -0.043 2.00e-02 2.50e+03 pdb=" HD1 TRP R 340 " -0.044 2.00e-02 2.50e+03 pdb=" HE1 TRP R 340 " 0.089 2.00e-02 2.50e+03 pdb=" HE3 TRP R 340 " 0.121 2.00e-02 2.50e+03 pdb=" HZ2 TRP R 340 " -0.109 2.00e-02 2.50e+03 pdb=" HZ3 TRP R 340 " 0.022 2.00e-02 2.50e+03 pdb=" HH2 TRP R 340 " -0.133 2.00e-02 2.50e+03 ... (remaining 11598 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 5469 2.18 - 2.78: 137996 2.78 - 3.39: 226717 3.39 - 3.99: 308893 3.99 - 4.60: 452584 Nonbonded interactions: 1131659 Sorted by model distance: nonbonded pdb=" OD2 ASP A 185 " pdb=" H1 HOH A 601 " model vdw 1.570 1.850 nonbonded pdb=" HH TYR A 246 " pdb=" OE2 GLU A 254 " model vdw 1.579 1.850 nonbonded pdb=" OE1 GLU O 270 " pdb=" HG1 THR P 202 " model vdw 1.587 1.850 nonbonded pdb=" OD1 ASP C 328 " pdb=" HG1 THR O 351 " model vdw 1.589 1.850 nonbonded pdb=" HG1 THR G 12 " pdb=" OE1 GLU G 13 " model vdw 1.590 1.850 ... (remaining 1131654 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 'H' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375)) selection = (chain 'I' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375)) selection = (chain 'M' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375)) selection = (chain 'N' and resid 6 through 375) selection = (chain 'O' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375)) selection = (chain 'P' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375)) selection = (chain 'Q' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375)) selection = (chain 'R' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.870 Extract box with map and model: 6.780 Check model and map are aligned: 0.860 Set scattering table: 0.530 Process input model: 196.230 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 211.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.012 0.144 39916 Z= 0.814 Angle : 1.910 23.514 54160 Z= 1.243 Chirality : 0.103 0.504 5990 Planarity : 0.018 0.403 6962 Dihedral : 15.069 154.603 14846 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.39 % Favored : 95.49 % Rotamer: Outliers : 2.29 % Allowed : 5.69 % Favored : 92.02 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % 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: -2.07 (0.11), residues: 4854 helix: -2.35 (0.09), residues: 1939 sheet: -0.65 (0.19), residues: 653 loop : -0.44 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.261 0.031 TRP M 340 HIS 0.015 0.004 HIS R 275 PHE 0.105 0.013 PHE D 196 TYR 0.181 0.019 TYR D 86 ARG 0.019 0.002 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 843 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 747 time to evaluate : 4.816 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: A 10 MET cc_start: 0.8999 (mtm) cc_final: 0.8521 (mtm) REVERT: A 130 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6279 (mt-10) REVERT: A 183 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7912 (p) REVERT: A 266 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7777 (mm) REVERT: A 276 HIS cc_start: 0.7315 (p90) cc_final: 0.7046 (p90) REVERT: A 321 ASP cc_start: 0.7949 (m-30) cc_final: 0.7745 (t0) REVERT: A 341 ASN cc_start: 0.8079 (t0) cc_final: 0.7465 (t0) REVERT: B 21 LYS cc_start: 0.8504 (mtmt) cc_final: 0.7813 (mmmt) REVERT: B 81 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8317 (mt-10) REVERT: B 224 GLU cc_start: 0.7941 (pt0) cc_final: 0.7484 (mp0) REVERT: B 237 MET cc_start: 0.8716 (mmm) cc_final: 0.8482 (mmm) REVERT: B 249 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8047 (mttm) REVERT: B 295 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7356 (ttp80) REVERT: B 305 MET cc_start: 0.9147 (mmm) cc_final: 0.8898 (mmt) REVERT: C 16 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7958 (tp30) REVERT: C 89 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7622 (p) REVERT: C 100 ASN cc_start: 0.8235 (t0) cc_final: 0.7854 (t0) REVERT: C 157 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7309 (p0) REVERT: C 159 VAL cc_start: 0.8899 (t) cc_final: 0.8619 (m) REVERT: C 167 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8023 (p0) REVERT: C 183 LYS cc_start: 0.8321 (mmtt) cc_final: 0.8041 (mmmm) REVERT: C 262 GLU cc_start: 0.7692 (pt0) cc_final: 0.7387 (tp30) REVERT: D 1 MET cc_start: 0.8723 (ptt) cc_final: 0.8504 (ptt) REVERT: D 106 GLN cc_start: 0.7615 (pt0) cc_final: 0.7346 (tm-30) REVERT: D 206 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7457 (mtt90) REVERT: D 215 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8415 (p) REVERT: D 225 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: D 230 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7532 (pt0) REVERT: D 247 GLU cc_start: 0.7917 (tp30) cc_final: 0.7554 (tp30) REVERT: D 286 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7830 (tptp) REVERT: E 79 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7278 (mt-10) REVERT: E 94 ARG cc_start: 0.7674 (mtp-110) cc_final: 0.7207 (mtm-85) REVERT: E 115 ASN cc_start: 0.8181 (t0) cc_final: 0.7951 (t0) REVERT: E 125 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: E 156 HIS cc_start: 0.8046 (t-90) cc_final: 0.7765 (t-90) REVERT: E 166 LYS cc_start: 0.7623 (mtpm) cc_final: 0.7381 (mmtt) REVERT: F 1 MET cc_start: 0.6103 (tmm) cc_final: 0.5784 (tmm) REVERT: F 84 ARG cc_start: 0.6910 (mtt-85) cc_final: 0.6695 (mtp-110) REVERT: F 88 ARG cc_start: 0.7627 (ttt-90) cc_final: 0.7227 (ttt-90) REVERT: F 107 LYS cc_start: 0.8146 (mmmm) cc_final: 0.7750 (mtpp) REVERT: G 19 GLN cc_start: 0.7899 (pm20) cc_final: 0.7561 (pm20) REVERT: G 88 ARG cc_start: 0.7705 (mmp80) cc_final: 0.7033 (mtm110) REVERT: G 124 SER cc_start: 0.8514 (t) cc_final: 0.8079 (m) REVERT: G 132 LYS cc_start: 0.8352 (mttm) cc_final: 0.8124 (mmtt) REVERT: H 68 LYS cc_start: 0.8178 (ptmt) cc_final: 0.7295 (mtmm) REVERT: H 100 GLU cc_start: 0.7522 (tt0) cc_final: 0.6959 (tm-30) REVERT: H 194 THR cc_start: 0.8668 (t) cc_final: 0.8456 (p) REVERT: H 227 MET cc_start: 0.8432 (mmm) cc_final: 0.8150 (mmm) REVERT: H 289 ILE cc_start: 0.8342 (mt) cc_final: 0.8070 (mt) REVERT: I 44 MET cc_start: 0.8768 (mtp) cc_final: 0.8364 (mtm) REVERT: I 149 THR cc_start: 0.5854 (m) cc_final: 0.5462 (t) REVERT: I 194 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8504 (p) REVERT: I 280 ASN cc_start: 0.7980 (m-40) cc_final: 0.7532 (m-40) REVERT: I 305 MET cc_start: 0.8426 (mmm) cc_final: 0.8159 (mmm) REVERT: M 119 MET cc_start: 0.8193 (ttm) cc_final: 0.7525 (ttm) REVERT: M 123 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.6918 (mpt) REVERT: M 337 TYR cc_start: 0.8191 (m-80) cc_final: 0.7894 (m-10) REVERT: N 54 VAL cc_start: 0.8095 (OUTLIER) cc_final: 0.7812 (m) REVERT: N 176 MET cc_start: 0.7868 (mtp) cc_final: 0.7631 (mtp) REVERT: N 270 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7880 (tt0) REVERT: O 81 ASP cc_start: 0.8426 (m-30) cc_final: 0.8152 (m-30) REVERT: O 82 MET cc_start: 0.8743 (tpt) cc_final: 0.8233 (tpt) REVERT: O 118 LYS cc_start: 0.7752 (mttm) cc_final: 0.7296 (mtpp) REVERT: O 132 MET cc_start: 0.8614 (ppp) cc_final: 0.8345 (ptm) REVERT: O 195 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: O 206 ARG cc_start: 0.7908 (ttp-170) cc_final: 0.7258 (ttm-80) REVERT: O 210 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7187 (ttp80) REVERT: O 222 ASP cc_start: 0.7932 (t0) cc_final: 0.7621 (p0) REVERT: O 227 MET cc_start: 0.8417 (tpt) cc_final: 0.8198 (mmm) REVERT: O 283 MET cc_start: 0.8899 (mmm) cc_final: 0.8498 (mmt) REVERT: O 287 ILE cc_start: 0.8489 (tt) cc_final: 0.8106 (mt) REVERT: O 289 ILE cc_start: 0.8729 (pt) cc_final: 0.8461 (pt) REVERT: O 292 ASP cc_start: 0.8273 (m-30) cc_final: 0.8031 (m-30) REVERT: O 305 MET cc_start: 0.8803 (mmm) cc_final: 0.8497 (mmm) REVERT: O 325 MET cc_start: 0.7962 (ptm) cc_final: 0.7597 (ptm) REVERT: O 326 LYS cc_start: 0.7906 (ptpp) cc_final: 0.7665 (mmtt) REVERT: O 328 LYS cc_start: 0.7556 (mtmt) cc_final: 0.7103 (mmmt) REVERT: O 372 ARG cc_start: 0.8435 (ptt-90) cc_final: 0.8081 (mtm110) REVERT: P 71 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8250 (mt) REVERT: P 72 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7161 (tt0) REVERT: P 81 ASP cc_start: 0.8203 (m-30) cc_final: 0.7877 (m-30) REVERT: P 82 MET cc_start: 0.9156 (tpt) cc_final: 0.8796 (tpt) REVERT: P 119 MET cc_start: 0.8217 (ttp) cc_final: 0.7887 (ttp) REVERT: P 194 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7757 (p) REVERT: P 205 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7393 (mt-10) REVERT: P 227 MET cc_start: 0.8725 (mmm) cc_final: 0.8192 (mmm) REVERT: P 313 MET cc_start: 0.8789 (tpt) cc_final: 0.8560 (mmm) REVERT: Q 9 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8607 (p) REVERT: Q 41 GLN cc_start: 0.6748 (mm-40) cc_final: 0.6341 (tp40) REVERT: Q 44 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8053 (mpt) REVERT: Q 49 GLN cc_start: 0.7542 (tt0) cc_final: 0.7151 (mm-40) REVERT: Q 54 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.9019 (t) REVERT: Q 105 LEU cc_start: 0.8522 (mt) cc_final: 0.8143 (mt) REVERT: Q 121 GLN cc_start: 0.7523 (tm-30) cc_final: 0.7073 (tt0) REVERT: Q 177 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8495 (tmt170) REVERT: Q 269 MET cc_start: 0.8721 (ptm) cc_final: 0.8463 (ptm) REVERT: Q 277 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8653 (t) REVERT: Q 284 LYS cc_start: 0.7937 (mttm) cc_final: 0.7603 (mtpt) REVERT: Q 291 LYS cc_start: 0.6205 (mttm) cc_final: 0.5601 (mmtt) REVERT: Q 326 LYS cc_start: 0.8067 (pttt) cc_final: 0.7801 (mmmm) REVERT: Q 328 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7419 (tptt) REVERT: R 116 ARG cc_start: 0.7954 (tpp80) cc_final: 0.7579 (mtp85) REVERT: R 227 MET cc_start: 0.8480 (mmm) cc_final: 0.8080 (mmm) REVERT: R 283 MET cc_start: 0.8796 (mmm) cc_final: 0.8453 (mmm) REVERT: R 286 ASP cc_start: 0.7468 (m-30) cc_final: 0.7082 (t0) REVERT: R 291 LYS cc_start: 0.8530 (ttpp) cc_final: 0.8043 (mmtp) REVERT: R 352 PHE cc_start: 0.8671 (t80) cc_final: 0.8184 (t80) outliers start: 96 outliers final: 28 residues processed: 811 average time/residue: 1.2064 time to fit residues: 1519.3107 Evaluate side-chains 537 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 489 time to evaluate : 4.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 2 PRO Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain M residue 123 MET Chi-restraints excluded: chain M residue 214 GLU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain O residue 12 ASN Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 194 THR Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 177 ARG Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 334 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 412 optimal weight: 0.9990 chunk 370 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 383 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 444 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN A 382 GLN B 83 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 GLN D 233 GLN F 92 GLN G 42 GLN G 48 GLN G 106 ASN I 246 GLN M 88 HIS O 162 ASN O 371 HIS P 128 ASN Q 246 GLN R 49 GLN R 297 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 39916 Z= 0.236 Angle : 0.695 7.476 54160 Z= 0.365 Chirality : 0.045 0.181 5990 Planarity : 0.006 0.129 6962 Dihedral : 10.809 159.303 5625 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.83 % Allowed : 8.65 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.32 (0.12), residues: 4854 helix: -1.45 (0.11), residues: 1985 sheet: -0.89 (0.16), residues: 935 loop : 0.14 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 86 HIS 0.007 0.001 HIS H 275 PHE 0.023 0.001 PHE B 277 TYR 0.019 0.001 TYR E 133 ARG 0.006 0.001 ARG R 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 578 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 501 time to evaluate : 4.845 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: A 73 ASP cc_start: 0.7245 (t0) cc_final: 0.6420 (t0) REVERT: A 146 MET cc_start: 0.8486 (mmm) cc_final: 0.8161 (mmm) REVERT: A 183 VAL cc_start: 0.8219 (OUTLIER) cc_final: 0.7970 (p) REVERT: A 276 HIS cc_start: 0.7435 (p90) cc_final: 0.7025 (p90) REVERT: B 21 LYS cc_start: 0.8579 (mtmt) cc_final: 0.7858 (mmmt) REVERT: B 224 GLU cc_start: 0.7644 (pt0) cc_final: 0.7251 (mt-10) REVERT: B 237 MET cc_start: 0.8639 (mmm) cc_final: 0.8381 (mmm) REVERT: B 249 LYS cc_start: 0.8307 (mtmt) cc_final: 0.7881 (mttm) REVERT: B 255 TYR cc_start: 0.8572 (p90) cc_final: 0.8175 (p90) REVERT: B 295 ARG cc_start: 0.7430 (mtp180) cc_final: 0.7142 (ttp80) REVERT: B 305 MET cc_start: 0.9087 (mmm) cc_final: 0.8845 (mmt) REVERT: C 16 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7912 (tp30) REVERT: C 55 ASP cc_start: 0.7652 (t0) cc_final: 0.7060 (m-30) REVERT: C 157 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.7058 (p0) REVERT: C 183 LYS cc_start: 0.8288 (mmtt) cc_final: 0.8034 (mmmm) REVERT: C 327 MET cc_start: 0.7638 (tpp) cc_final: 0.7144 (tpt) REVERT: C 347 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8600 (pt) REVERT: D 106 GLN cc_start: 0.7593 (pt0) cc_final: 0.7380 (tm-30) REVERT: D 113 MET cc_start: 0.8295 (tpp) cc_final: 0.7536 (mmt) REVERT: D 117 ASN cc_start: 0.8080 (m-40) cc_final: 0.7805 (m110) REVERT: D 157 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7097 (mpp) REVERT: D 206 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7243 (mtm110) REVERT: D 230 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7239 (pt0) REVERT: D 247 GLU cc_start: 0.7974 (tp30) cc_final: 0.7590 (tp30) REVERT: E 79 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6728 (mt-10) REVERT: E 94 ARG cc_start: 0.7700 (mtp-110) cc_final: 0.7217 (mtm-85) REVERT: E 128 GLU cc_start: 0.8364 (tp30) cc_final: 0.8163 (tp30) REVERT: E 156 HIS cc_start: 0.7655 (t-90) cc_final: 0.7101 (t-90) REVERT: G 19 GLN cc_start: 0.7874 (pm20) cc_final: 0.7593 (pm20) REVERT: G 30 GLU cc_start: 0.8134 (mp0) cc_final: 0.7491 (tm-30) REVERT: G 88 ARG cc_start: 0.7425 (mmp80) cc_final: 0.6701 (mtm110) REVERT: G 124 SER cc_start: 0.7784 (t) cc_final: 0.7408 (m) REVERT: H 68 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7490 (mttp) REVERT: H 95 ARG cc_start: 0.7307 (mtt-85) cc_final: 0.7102 (mtt-85) REVERT: H 100 GLU cc_start: 0.7340 (tt0) cc_final: 0.6744 (tm-30) REVERT: H 107 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6677 (tm-30) REVERT: H 119 MET cc_start: 0.7982 (ttm) cc_final: 0.7737 (ttp) REVERT: H 169 TYR cc_start: 0.8276 (m-80) cc_final: 0.7848 (m-10) REVERT: H 190 MET cc_start: 0.8421 (mtp) cc_final: 0.8180 (ttm) REVERT: H 194 THR cc_start: 0.8761 (t) cc_final: 0.8476 (p) REVERT: H 305 MET cc_start: 0.8683 (tpt) cc_final: 0.8434 (tpt) REVERT: I 44 MET cc_start: 0.8450 (mtp) cc_final: 0.8212 (mtm) REVERT: I 132 MET cc_start: 0.7612 (pmm) cc_final: 0.7275 (pmm) REVERT: I 194 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8437 (p) REVERT: I 280 ASN cc_start: 0.7997 (m-40) cc_final: 0.7744 (m-40) REVERT: M 211 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: N 54 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7840 (m) REVERT: N 270 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7642 (tt0) REVERT: O 57 GLU cc_start: 0.7598 (tt0) cc_final: 0.7239 (tp30) REVERT: O 81 ASP cc_start: 0.8497 (m-30) cc_final: 0.8281 (m-30) REVERT: O 82 MET cc_start: 0.8695 (tpt) cc_final: 0.8406 (tpt) REVERT: O 118 LYS cc_start: 0.7641 (mttm) cc_final: 0.7184 (mtpp) REVERT: O 222 ASP cc_start: 0.7901 (t0) cc_final: 0.7658 (p0) REVERT: O 283 MET cc_start: 0.8829 (mmm) cc_final: 0.8342 (mmt) REVERT: O 287 ILE cc_start: 0.8392 (tt) cc_final: 0.8064 (mt) REVERT: O 292 ASP cc_start: 0.8408 (m-30) cc_final: 0.8118 (m-30) REVERT: O 305 MET cc_start: 0.8671 (mmm) cc_final: 0.8304 (mmm) REVERT: O 325 MET cc_start: 0.8026 (ptm) cc_final: 0.7577 (ptm) REVERT: P 47 MET cc_start: 0.3647 (mmm) cc_final: 0.3414 (mmt) REVERT: P 72 GLU cc_start: 0.7660 (mm-30) cc_final: 0.6954 (tt0) REVERT: P 82 MET cc_start: 0.9086 (tpt) cc_final: 0.8796 (tpt) REVERT: P 119 MET cc_start: 0.7807 (ttp) cc_final: 0.7402 (ttp) REVERT: P 176 MET cc_start: 0.8551 (mmp) cc_final: 0.8148 (mmm) REVERT: P 205 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6999 (mt-10) REVERT: P 227 MET cc_start: 0.8550 (mmm) cc_final: 0.8180 (mmm) REVERT: P 326 LYS cc_start: 0.7957 (pttp) cc_final: 0.7681 (ptmm) REVERT: Q 41 GLN cc_start: 0.6134 (mm-40) cc_final: 0.5916 (tp40) REVERT: Q 44 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.7747 (mpt) REVERT: Q 47 MET cc_start: 0.8380 (mmm) cc_final: 0.7240 (ptt) REVERT: Q 54 VAL cc_start: 0.9411 (OUTLIER) cc_final: 0.9160 (t) REVERT: Q 103 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8077 (p) REVERT: Q 105 LEU cc_start: 0.8172 (mt) cc_final: 0.7910 (mt) REVERT: Q 269 MET cc_start: 0.8700 (ptm) cc_final: 0.8488 (ptm) REVERT: Q 277 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8255 (t) REVERT: Q 291 LYS cc_start: 0.6061 (mttm) cc_final: 0.5634 (mmtt) REVERT: Q 326 LYS cc_start: 0.7895 (pttt) cc_final: 0.7552 (mmtm) REVERT: Q 328 LYS cc_start: 0.7605 (ttmt) cc_final: 0.7372 (ttmm) REVERT: Q 372 ARG cc_start: 0.7729 (ptt90) cc_final: 0.7493 (ptt90) REVERT: R 82 MET cc_start: 0.8432 (mmm) cc_final: 0.7496 (tpt) REVERT: R 175 ILE cc_start: 0.8764 (mt) cc_final: 0.8498 (mt) REVERT: R 227 MET cc_start: 0.8441 (mmm) cc_final: 0.7926 (mmm) REVERT: R 286 ASP cc_start: 0.7567 (m-30) cc_final: 0.7061 (t0) REVERT: R 291 LYS cc_start: 0.8452 (ttpp) cc_final: 0.7987 (mmtt) outliers start: 77 outliers final: 42 residues processed: 556 average time/residue: 1.2008 time to fit residues: 1039.6694 Evaluate side-chains 467 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 413 time to evaluate : 4.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 253 GLU Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 211 ASP Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 177 ARG Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 358 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 246 optimal weight: 0.0770 chunk 137 optimal weight: 2.9990 chunk 369 optimal weight: 0.7980 chunk 302 optimal weight: 2.9990 chunk 122 optimal weight: 0.0970 chunk 444 optimal weight: 2.9990 chunk 480 optimal weight: 0.0970 chunk 396 optimal weight: 2.9990 chunk 441 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 356 optimal weight: 3.9990 overall best weight: 0.8136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN E 115 ASN H 297 ASN M 297 ASN N 162 ASN N 296 ASN O 360 GLN P 162 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 39916 Z= 0.164 Angle : 0.585 6.879 54160 Z= 0.296 Chirality : 0.043 0.161 5990 Planarity : 0.004 0.075 6962 Dihedral : 9.593 171.616 5585 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.48 % Allowed : 10.03 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.12), residues: 4854 helix: -0.82 (0.11), residues: 1987 sheet: -0.85 (0.16), residues: 931 loop : 0.37 (0.15), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 86 HIS 0.006 0.001 HIS M 87 PHE 0.017 0.001 PHE B 277 TYR 0.014 0.001 TYR P 143 ARG 0.006 0.000 ARG P 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 511 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 449 time to evaluate : 4.860 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: A 148 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7399 (mt-10) REVERT: A 183 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7976 (p) REVERT: A 276 HIS cc_start: 0.7446 (p90) cc_final: 0.6978 (p90) REVERT: A 359 HIS cc_start: 0.6889 (t-170) cc_final: 0.6553 (t70) REVERT: A 406 LYS cc_start: 0.8237 (pttp) cc_final: 0.7859 (ttpp) REVERT: B 21 LYS cc_start: 0.8560 (mtmt) cc_final: 0.7772 (mmmt) REVERT: B 51 ASP cc_start: 0.8295 (m-30) cc_final: 0.7662 (t0) REVERT: B 72 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6723 (tt0) REVERT: B 224 GLU cc_start: 0.7481 (pt0) cc_final: 0.7201 (mt-10) REVERT: B 237 MET cc_start: 0.8647 (mmm) cc_final: 0.8435 (mmm) REVERT: B 249 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7752 (mtpp) REVERT: B 255 TYR cc_start: 0.8622 (p90) cc_final: 0.8289 (p90) REVERT: B 295 ARG cc_start: 0.7491 (mtp180) cc_final: 0.7024 (ttm170) REVERT: B 305 MET cc_start: 0.9100 (mmm) cc_final: 0.8747 (mmt) REVERT: C 16 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7928 (tp30) REVERT: C 55 ASP cc_start: 0.7648 (t0) cc_final: 0.7037 (m-30) REVERT: C 157 ASN cc_start: 0.7341 (OUTLIER) cc_final: 0.6994 (p0) REVERT: C 183 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7986 (mmmm) REVERT: C 347 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8457 (pt) REVERT: D 206 ARG cc_start: 0.7741 (mtm-85) cc_final: 0.7187 (mtm110) REVERT: D 230 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7401 (pt0) REVERT: D 247 GLU cc_start: 0.7987 (tp30) cc_final: 0.7601 (tp30) REVERT: E 79 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6757 (mt-10) REVERT: E 94 ARG cc_start: 0.7633 (mtp-110) cc_final: 0.7180 (mtm-85) REVERT: F 88 ARG cc_start: 0.7557 (ttt-90) cc_final: 0.7205 (ttt-90) REVERT: G 19 GLN cc_start: 0.7788 (pm20) cc_final: 0.7496 (pm20) REVERT: G 30 GLU cc_start: 0.8110 (mp0) cc_final: 0.7543 (tm-30) REVERT: G 88 ARG cc_start: 0.7171 (mmp80) cc_final: 0.6480 (mtm110) REVERT: G 124 SER cc_start: 0.7740 (t) cc_final: 0.7393 (m) REVERT: H 47 MET cc_start: 0.6317 (mmt) cc_final: 0.6009 (mmt) REVERT: H 68 LYS cc_start: 0.8087 (ptmt) cc_final: 0.7431 (mttp) REVERT: H 95 ARG cc_start: 0.7315 (mtt-85) cc_final: 0.7104 (mtt-85) REVERT: H 100 GLU cc_start: 0.7275 (tt0) cc_final: 0.6865 (tm-30) REVERT: H 194 THR cc_start: 0.8796 (t) cc_final: 0.8467 (p) REVERT: I 194 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8422 (p) REVERT: I 280 ASN cc_start: 0.8099 (m-40) cc_final: 0.7812 (m-40) REVERT: M 90 PHE cc_start: 0.8108 (m-80) cc_final: 0.7501 (m-80) REVERT: M 119 MET cc_start: 0.7670 (ttm) cc_final: 0.7445 (ttm) REVERT: M 167 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6806 (tm-30) REVERT: M 211 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8125 (m-30) REVERT: N 54 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7905 (m) REVERT: N 270 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7927 (tt0) REVERT: O 57 GLU cc_start: 0.7571 (tt0) cc_final: 0.7152 (tp30) REVERT: O 82 MET cc_start: 0.8657 (tpt) cc_final: 0.8441 (tpt) REVERT: O 118 LYS cc_start: 0.7629 (mttm) cc_final: 0.7148 (mtpp) REVERT: O 222 ASP cc_start: 0.7890 (t0) cc_final: 0.7640 (p0) REVERT: O 283 MET cc_start: 0.8770 (mmm) cc_final: 0.8334 (mmt) REVERT: O 287 ILE cc_start: 0.8287 (tt) cc_final: 0.7880 (mt) REVERT: O 292 ASP cc_start: 0.8414 (m-30) cc_final: 0.7961 (m-30) REVERT: O 305 MET cc_start: 0.8649 (mmm) cc_final: 0.8295 (mmm) REVERT: O 325 MET cc_start: 0.7845 (ptm) cc_final: 0.7310 (ptm) REVERT: P 72 GLU cc_start: 0.7643 (mm-30) cc_final: 0.6944 (tt0) REVERT: P 165 ILE cc_start: 0.8701 (mt) cc_final: 0.8496 (mt) REVERT: P 176 MET cc_start: 0.8607 (mmp) cc_final: 0.8298 (mmm) REVERT: P 206 ARG cc_start: 0.8079 (tmm-80) cc_final: 0.7734 (ttm-80) REVERT: P 326 LYS cc_start: 0.7885 (pttp) cc_final: 0.7637 (ptmm) REVERT: Q 41 GLN cc_start: 0.6659 (mm-40) cc_final: 0.6295 (tp40) REVERT: Q 44 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.7778 (mpt) REVERT: Q 47 MET cc_start: 0.8345 (mmm) cc_final: 0.7193 (ptt) REVERT: Q 54 VAL cc_start: 0.9381 (p) cc_final: 0.9153 (t) REVERT: Q 105 LEU cc_start: 0.8322 (mt) cc_final: 0.8063 (mt) REVERT: Q 277 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8191 (t) REVERT: Q 291 LYS cc_start: 0.6049 (mttm) cc_final: 0.5221 (mmtt) REVERT: Q 326 LYS cc_start: 0.7852 (pttt) cc_final: 0.7492 (mmmm) REVERT: Q 328 LYS cc_start: 0.7591 (ttmt) cc_final: 0.7095 (tptt) REVERT: R 82 MET cc_start: 0.8380 (mmm) cc_final: 0.7331 (tpt) REVERT: R 286 ASP cc_start: 0.7467 (m-30) cc_final: 0.6963 (t0) REVERT: R 291 LYS cc_start: 0.8416 (ttpp) cc_final: 0.8012 (mmtt) outliers start: 62 outliers final: 39 residues processed: 495 average time/residue: 1.1578 time to fit residues: 908.2009 Evaluate side-chains 451 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 404 time to evaluate : 4.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 211 ASP Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 177 ARG Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 358 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 439 optimal weight: 4.9990 chunk 334 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 chunk 446 optimal weight: 1.9990 chunk 472 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 423 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 124 HIS ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS E 139 GLN G 130 HIS H 162 ASN P 162 ASN Q 162 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 39916 Z= 0.434 Angle : 0.645 8.267 54160 Z= 0.329 Chirality : 0.047 0.173 5990 Planarity : 0.005 0.064 6962 Dihedral : 9.396 176.034 5578 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.86 % Allowed : 10.36 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.85 (0.12), residues: 4854 helix: -0.76 (0.11), residues: 1983 sheet: -0.93 (0.16), residues: 944 loop : 0.20 (0.15), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 356 HIS 0.009 0.001 HIS R 371 PHE 0.022 0.002 PHE B 277 TYR 0.016 0.002 TYR F 8 ARG 0.007 0.001 ARG P 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 475 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 397 time to evaluate : 4.810 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: A 137 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6583 (mp0) REVERT: A 148 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7819 (mt-10) REVERT: A 276 HIS cc_start: 0.7423 (p90) cc_final: 0.6833 (p90) REVERT: A 406 LYS cc_start: 0.8176 (pttp) cc_final: 0.7888 (ttpp) REVERT: B 21 LYS cc_start: 0.8431 (mtmt) cc_final: 0.7669 (mmmt) REVERT: B 51 ASP cc_start: 0.8401 (m-30) cc_final: 0.7689 (t0) REVERT: B 72 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6538 (tt0) REVERT: B 224 GLU cc_start: 0.7560 (pt0) cc_final: 0.7235 (mt-10) REVERT: B 237 MET cc_start: 0.8726 (mmm) cc_final: 0.8504 (mmm) REVERT: B 249 LYS cc_start: 0.8462 (mtmt) cc_final: 0.7909 (mtpp) REVERT: B 295 ARG cc_start: 0.7541 (mtp180) cc_final: 0.7084 (ttm170) REVERT: B 365 ASP cc_start: 0.8286 (t0) cc_final: 0.8017 (m-30) REVERT: C 16 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7950 (tp30) REVERT: C 55 ASP cc_start: 0.7650 (t0) cc_final: 0.7069 (m-30) REVERT: C 157 ASN cc_start: 0.7082 (OUTLIER) cc_final: 0.6716 (p0) REVERT: C 183 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7997 (mmmm) REVERT: D 206 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7269 (mtm110) REVERT: D 230 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7334 (pt0) REVERT: E 79 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6763 (mt-10) REVERT: E 94 ARG cc_start: 0.7897 (mtp-110) cc_final: 0.7278 (mtm-85) REVERT: E 156 HIS cc_start: 0.7637 (t-90) cc_final: 0.7300 (t-90) REVERT: F 88 ARG cc_start: 0.7597 (ttt-90) cc_final: 0.7224 (ttt-90) REVERT: F 126 MET cc_start: 0.9101 (mtp) cc_final: 0.8831 (mtm) REVERT: G 19 GLN cc_start: 0.7829 (pm20) cc_final: 0.7524 (pm20) REVERT: G 30 GLU cc_start: 0.8099 (mp0) cc_final: 0.7541 (tm-30) REVERT: G 88 ARG cc_start: 0.7439 (mmp80) cc_final: 0.6711 (mtm110) REVERT: G 124 SER cc_start: 0.7812 (t) cc_final: 0.7469 (m) REVERT: H 68 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7315 (mttm) REVERT: H 100 GLU cc_start: 0.7261 (tt0) cc_final: 0.6826 (tm-30) REVERT: H 194 THR cc_start: 0.8809 (t) cc_final: 0.8514 (p) REVERT: I 269 MET cc_start: 0.8098 (mtp) cc_final: 0.7738 (mtp) REVERT: M 90 PHE cc_start: 0.8152 (m-80) cc_final: 0.7626 (m-80) REVERT: M 119 MET cc_start: 0.7666 (ttm) cc_final: 0.7459 (ttm) REVERT: M 167 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7059 (tm-30) REVERT: M 211 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8315 (m-30) REVERT: M 299 MET cc_start: 0.8688 (mtm) cc_final: 0.8478 (mtm) REVERT: N 54 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.8013 (m) REVERT: O 57 GLU cc_start: 0.7522 (tt0) cc_final: 0.7116 (tp30) REVERT: O 118 LYS cc_start: 0.7659 (mttm) cc_final: 0.7207 (mtpp) REVERT: O 222 ASP cc_start: 0.7878 (t0) cc_final: 0.7419 (p0) REVERT: O 283 MET cc_start: 0.8761 (mmm) cc_final: 0.8375 (mmt) REVERT: O 287 ILE cc_start: 0.8509 (tt) cc_final: 0.8181 (mt) REVERT: O 292 ASP cc_start: 0.8554 (m-30) cc_final: 0.8046 (m-30) REVERT: O 325 MET cc_start: 0.7979 (ptm) cc_final: 0.7554 (ptm) REVERT: P 72 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7302 (tt0) REVERT: P 82 MET cc_start: 0.9024 (tpt) cc_final: 0.8816 (tpt) REVERT: P 123 MET cc_start: 0.8720 (tpp) cc_final: 0.8187 (mmt) REVERT: P 165 ILE cc_start: 0.8753 (mt) cc_final: 0.8533 (mt) REVERT: P 176 MET cc_start: 0.8648 (mmp) cc_final: 0.8344 (mmm) REVERT: P 206 ARG cc_start: 0.8205 (tmm-80) cc_final: 0.7870 (ttm-80) REVERT: P 326 LYS cc_start: 0.8211 (pttp) cc_final: 0.7924 (ptmm) REVERT: Q 44 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.7547 (mpt) REVERT: Q 47 MET cc_start: 0.8355 (mmm) cc_final: 0.7335 (ptt) REVERT: Q 103 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8049 (p) REVERT: Q 105 LEU cc_start: 0.8449 (mt) cc_final: 0.8145 (mt) REVERT: Q 177 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8562 (ttt180) REVERT: Q 291 LYS cc_start: 0.6196 (mttm) cc_final: 0.5566 (mmtt) REVERT: Q 326 LYS cc_start: 0.7954 (pttt) cc_final: 0.7603 (mmtm) REVERT: R 45 VAL cc_start: 0.7708 (p) cc_final: 0.7491 (p) REVERT: R 283 MET cc_start: 0.8643 (mmm) cc_final: 0.7901 (mmp) REVERT: R 286 ASP cc_start: 0.7451 (m-30) cc_final: 0.6920 (t0) REVERT: R 291 LYS cc_start: 0.8448 (ttpp) cc_final: 0.8088 (mmtt) outliers start: 78 outliers final: 54 residues processed: 456 average time/residue: 1.1054 time to fit residues: 787.3907 Evaluate side-chains 443 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 380 time to evaluate : 4.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 211 ASP Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 177 ARG Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 194 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 393 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 351 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 403 optimal weight: 1.9990 chunk 326 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 424 optimal weight: 0.4980 chunk 119 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN N 162 ASN Q 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39916 Z= 0.206 Angle : 0.562 6.782 54160 Z= 0.280 Chirality : 0.043 0.150 5990 Planarity : 0.004 0.069 6962 Dihedral : 8.843 156.898 5570 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.72 % Allowed : 10.70 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.12), residues: 4854 helix: -0.46 (0.12), residues: 1979 sheet: -0.77 (0.17), residues: 898 loop : 0.23 (0.15), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 356 HIS 0.006 0.001 HIS D 270 PHE 0.015 0.001 PHE B 277 TYR 0.013 0.001 TYR P 143 ARG 0.006 0.000 ARG P 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 470 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 398 time to evaluate : 4.826 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: A 276 HIS cc_start: 0.7373 (p90) cc_final: 0.6720 (p90) REVERT: A 363 MET cc_start: 0.7920 (mmm) cc_final: 0.7373 (mtp) REVERT: A 406 LYS cc_start: 0.8204 (pttp) cc_final: 0.7927 (ttpp) REVERT: B 6 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7301 (mt) REVERT: B 51 ASP cc_start: 0.8400 (m-30) cc_final: 0.7708 (t0) REVERT: B 72 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6525 (tt0) REVERT: B 224 GLU cc_start: 0.7437 (pt0) cc_final: 0.7185 (mt-10) REVERT: B 249 LYS cc_start: 0.8391 (mtmt) cc_final: 0.7830 (mtpp) REVERT: B 255 TYR cc_start: 0.8740 (p90) cc_final: 0.8313 (p90) REVERT: B 295 ARG cc_start: 0.7504 (mtp180) cc_final: 0.7039 (ttm170) REVERT: B 365 ASP cc_start: 0.8268 (t0) cc_final: 0.8032 (m-30) REVERT: B 367 MET cc_start: 0.8043 (tpt) cc_final: 0.7809 (tpp) REVERT: C 55 ASP cc_start: 0.7568 (t0) cc_final: 0.7004 (m-30) REVERT: C 157 ASN cc_start: 0.7125 (OUTLIER) cc_final: 0.6787 (p0) REVERT: C 183 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7979 (mmmm) REVERT: D 206 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7258 (mtm110) REVERT: D 230 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7389 (pt0) REVERT: E 79 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6623 (mt-10) REVERT: E 94 ARG cc_start: 0.7871 (mtp-110) cc_final: 0.7245 (mtm-85) REVERT: F 88 ARG cc_start: 0.7511 (ttt-90) cc_final: 0.7159 (ttt-90) REVERT: F 126 MET cc_start: 0.9035 (mtp) cc_final: 0.8834 (mtm) REVERT: G 19 GLN cc_start: 0.7750 (pm20) cc_final: 0.7478 (pm20) REVERT: G 30 GLU cc_start: 0.8084 (mp0) cc_final: 0.7527 (tm-30) REVERT: G 88 ARG cc_start: 0.7487 (mmp80) cc_final: 0.6710 (mtm110) REVERT: G 124 SER cc_start: 0.7731 (t) cc_final: 0.7423 (m) REVERT: H 68 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7322 (mttm) REVERT: H 100 GLU cc_start: 0.7248 (tt0) cc_final: 0.6780 (tm-30) REVERT: H 194 THR cc_start: 0.8783 (t) cc_final: 0.8536 (p) REVERT: M 90 PHE cc_start: 0.8121 (m-80) cc_final: 0.7593 (m-80) REVERT: M 119 MET cc_start: 0.7553 (ttm) cc_final: 0.7352 (ttm) REVERT: M 123 MET cc_start: 0.8990 (mmt) cc_final: 0.8435 (mmt) REVERT: M 167 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7054 (tm-30) REVERT: M 211 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8244 (m-30) REVERT: M 299 MET cc_start: 0.8695 (mtm) cc_final: 0.8491 (mtm) REVERT: N 54 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.8026 (m) REVERT: O 57 GLU cc_start: 0.7504 (tt0) cc_final: 0.7137 (tp30) REVERT: O 118 LYS cc_start: 0.7639 (mttm) cc_final: 0.7137 (mtpp) REVERT: O 222 ASP cc_start: 0.7833 (t0) cc_final: 0.7385 (p0) REVERT: O 283 MET cc_start: 0.8742 (mmm) cc_final: 0.8318 (mmt) REVERT: O 287 ILE cc_start: 0.8478 (tt) cc_final: 0.8126 (mt) REVERT: O 292 ASP cc_start: 0.8521 (m-30) cc_final: 0.7923 (m-30) REVERT: O 325 MET cc_start: 0.7846 (ptm) cc_final: 0.7329 (ptm) REVERT: P 72 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7227 (tt0) REVERT: P 123 MET cc_start: 0.8765 (tpp) cc_final: 0.8246 (mmt) REVERT: P 165 ILE cc_start: 0.8739 (mt) cc_final: 0.8536 (mt) REVERT: P 176 MET cc_start: 0.8586 (mmp) cc_final: 0.8329 (mmm) REVERT: P 206 ARG cc_start: 0.8119 (tmm-80) cc_final: 0.7799 (ttm-80) REVERT: P 326 LYS cc_start: 0.8169 (pttp) cc_final: 0.7944 (ptmm) REVERT: Q 44 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.7594 (mpt) REVERT: Q 47 MET cc_start: 0.8256 (mmm) cc_final: 0.7329 (ptt) REVERT: Q 103 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8112 (p) REVERT: Q 105 LEU cc_start: 0.8349 (mt) cc_final: 0.8051 (mt) REVERT: Q 205 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7315 (mt-10) REVERT: Q 291 LYS cc_start: 0.5918 (mttm) cc_final: 0.5312 (mmtt) REVERT: Q 326 LYS cc_start: 0.7907 (pttt) cc_final: 0.7519 (mmtm) REVERT: Q 328 LYS cc_start: 0.7433 (ttmm) cc_final: 0.6831 (tptt) REVERT: R 283 MET cc_start: 0.8471 (mmm) cc_final: 0.7745 (mmp) REVERT: R 286 ASP cc_start: 0.7511 (m-30) cc_final: 0.6957 (t0) REVERT: R 291 LYS cc_start: 0.8429 (ttpp) cc_final: 0.8078 (mmtt) outliers start: 72 outliers final: 52 residues processed: 453 average time/residue: 1.1589 time to fit residues: 828.9178 Evaluate side-chains 447 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 388 time to evaluate : 4.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 211 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 159 optimal weight: 3.9990 chunk 425 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 277 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 473 optimal weight: 3.9990 chunk 392 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS E 115 ASN E 156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 39916 Z= 0.304 Angle : 0.576 6.907 54160 Z= 0.289 Chirality : 0.044 0.158 5990 Planarity : 0.004 0.063 6962 Dihedral : 8.651 158.701 5566 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.88 % Allowed : 10.93 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.12), residues: 4854 helix: -0.40 (0.12), residues: 1980 sheet: -0.81 (0.17), residues: 898 loop : 0.18 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 356 HIS 0.009 0.001 HIS E 156 PHE 0.017 0.001 PHE B 277 TYR 0.011 0.001 TYR E 133 ARG 0.007 0.000 ARG P 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 469 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 390 time to evaluate : 6.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7703 (mt-10) REVERT: A 276 HIS cc_start: 0.7473 (p90) cc_final: 0.6763 (p90) REVERT: A 363 MET cc_start: 0.7902 (mmm) cc_final: 0.7416 (mtp) REVERT: A 406 LYS cc_start: 0.8154 (pttp) cc_final: 0.7900 (ttpp) REVERT: B 6 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7302 (mt) REVERT: B 51 ASP cc_start: 0.8383 (m-30) cc_final: 0.7705 (t0) REVERT: B 82 MET cc_start: 0.7944 (tpt) cc_final: 0.7454 (tpt) REVERT: B 224 GLU cc_start: 0.7434 (pt0) cc_final: 0.7189 (mt-10) REVERT: B 249 LYS cc_start: 0.8429 (mtmt) cc_final: 0.7833 (mtpp) REVERT: B 295 ARG cc_start: 0.7516 (mtp180) cc_final: 0.7039 (ttm170) REVERT: B 341 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: B 365 ASP cc_start: 0.8202 (t0) cc_final: 0.7936 (m-30) REVERT: C 55 ASP cc_start: 0.7531 (t0) cc_final: 0.6983 (m-30) REVERT: C 83 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6925 (pt0) REVERT: C 157 ASN cc_start: 0.6996 (OUTLIER) cc_final: 0.6680 (p0) REVERT: C 183 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7980 (mmmm) REVERT: C 251 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7646 (mt0) REVERT: D 206 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7296 (mtm110) REVERT: D 230 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7345 (pt0) REVERT: E 79 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6768 (mt-10) REVERT: E 94 ARG cc_start: 0.7895 (mtp-110) cc_final: 0.7309 (mtm-85) REVERT: F 88 ARG cc_start: 0.7481 (ttt-90) cc_final: 0.7221 (ttt-90) REVERT: G 19 GLN cc_start: 0.7753 (pm20) cc_final: 0.7438 (pm20) REVERT: G 30 GLU cc_start: 0.8116 (mp0) cc_final: 0.7558 (tm-30) REVERT: G 88 ARG cc_start: 0.7418 (mmp80) cc_final: 0.6699 (mtm110) REVERT: G 124 SER cc_start: 0.7765 (t) cc_final: 0.7463 (m) REVERT: H 68 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7320 (mttm) REVERT: H 100 GLU cc_start: 0.7267 (tt0) cc_final: 0.6788 (tm-30) REVERT: H 107 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7478 (tm-30) REVERT: H 194 THR cc_start: 0.8828 (t) cc_final: 0.8535 (p) REVERT: M 90 PHE cc_start: 0.8144 (m-80) cc_final: 0.7631 (m-80) REVERT: M 123 MET cc_start: 0.8962 (mmt) cc_final: 0.8524 (mmt) REVERT: M 167 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7224 (tm-30) REVERT: M 211 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: N 54 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.8063 (m) REVERT: O 57 GLU cc_start: 0.7516 (tt0) cc_final: 0.7150 (tp30) REVERT: O 222 ASP cc_start: 0.7817 (t0) cc_final: 0.7320 (p0) REVERT: O 283 MET cc_start: 0.8750 (mmm) cc_final: 0.8343 (mmt) REVERT: O 287 ILE cc_start: 0.8512 (tt) cc_final: 0.8139 (mt) REVERT: O 292 ASP cc_start: 0.8526 (m-30) cc_final: 0.7928 (m-30) REVERT: P 72 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7316 (tt0) REVERT: P 82 MET cc_start: 0.8978 (tpt) cc_final: 0.8632 (tpp) REVERT: P 123 MET cc_start: 0.8792 (tpp) cc_final: 0.8289 (mmt) REVERT: P 125 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7517 (mm-30) REVERT: P 165 ILE cc_start: 0.8746 (mt) cc_final: 0.8537 (mt) REVERT: P 176 MET cc_start: 0.8639 (mmp) cc_final: 0.8379 (mmm) REVERT: P 206 ARG cc_start: 0.8228 (tmm-80) cc_final: 0.7928 (ttm-80) REVERT: P 326 LYS cc_start: 0.8122 (pttp) cc_final: 0.7823 (ptmm) REVERT: Q 47 MET cc_start: 0.8205 (mmm) cc_final: 0.7273 (ptt) REVERT: Q 54 VAL cc_start: 0.9411 (OUTLIER) cc_final: 0.9211 (p) REVERT: Q 103 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8172 (p) REVERT: Q 105 LEU cc_start: 0.8281 (mt) cc_final: 0.7958 (mt) REVERT: Q 205 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7433 (mt-10) REVERT: Q 291 LYS cc_start: 0.5978 (mttm) cc_final: 0.5246 (mmtt) REVERT: Q 326 LYS cc_start: 0.7939 (pttt) cc_final: 0.7548 (mmtm) REVERT: Q 372 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7250 (ptt90) REVERT: R 75 ILE cc_start: 0.8621 (pt) cc_final: 0.8272 (pt) REVERT: R 283 MET cc_start: 0.8466 (mmm) cc_final: 0.7635 (mmp) REVERT: R 286 ASP cc_start: 0.7503 (m-30) cc_final: 0.6966 (t0) REVERT: R 291 LYS cc_start: 0.8435 (ttpp) cc_final: 0.8090 (mmtt) outliers start: 79 outliers final: 56 residues processed: 450 average time/residue: 1.1061 time to fit residues: 786.5989 Evaluate side-chains 447 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 379 time to evaluate : 4.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 176 MET Chi-restraints excluded: chain M residue 211 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain Q residue 372 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 456 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 269 optimal weight: 1.9990 chunk 345 optimal weight: 0.4980 chunk 267 optimal weight: 9.9990 chunk 398 optimal weight: 2.9990 chunk 264 optimal weight: 9.9990 chunk 471 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS H 87 HIS M 161 HIS M 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 39916 Z= 0.356 Angle : 0.600 7.142 54160 Z= 0.301 Chirality : 0.045 0.156 5990 Planarity : 0.004 0.059 6962 Dihedral : 8.536 157.309 5563 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.02 % Allowed : 11.15 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.12), residues: 4854 helix: -0.38 (0.12), residues: 1969 sheet: -1.11 (0.17), residues: 868 loop : 0.15 (0.14), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Q 356 HIS 0.009 0.001 HIS E 156 PHE 0.017 0.002 PHE B 277 TYR 0.018 0.001 TYR R 294 ARG 0.008 0.001 ARG I 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 476 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 391 time to evaluate : 4.816 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: A 137 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6551 (mp0) REVERT: A 148 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7638 (mt-10) REVERT: A 262 PRO cc_start: 0.8531 (Cg_endo) cc_final: 0.8278 (Cg_exo) REVERT: A 276 HIS cc_start: 0.7444 (p90) cc_final: 0.6749 (p90) REVERT: A 300 SER cc_start: 0.8859 (t) cc_final: 0.8318 (p) REVERT: A 363 MET cc_start: 0.8170 (mmm) cc_final: 0.7860 (mtp) REVERT: A 406 LYS cc_start: 0.8125 (pttp) cc_final: 0.7859 (ttpp) REVERT: B 6 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7298 (mt) REVERT: B 51 ASP cc_start: 0.8204 (m-30) cc_final: 0.7624 (t0) REVERT: B 102 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6841 (ptpp) REVERT: B 224 GLU cc_start: 0.7488 (pt0) cc_final: 0.7187 (mt-10) REVERT: B 249 LYS cc_start: 0.8590 (mtmt) cc_final: 0.7964 (mtpp) REVERT: B 295 ARG cc_start: 0.7549 (mtp180) cc_final: 0.7067 (ttm170) REVERT: B 341 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: B 365 ASP cc_start: 0.8181 (t0) cc_final: 0.7832 (m-30) REVERT: C 55 ASP cc_start: 0.7486 (t0) cc_final: 0.6928 (m-30) REVERT: C 157 ASN cc_start: 0.6970 (OUTLIER) cc_final: 0.6667 (p0) REVERT: C 183 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7950 (mmmm) REVERT: C 251 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7683 (mt0) REVERT: D 206 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7308 (mtm110) REVERT: D 230 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7393 (pt0) REVERT: E 79 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6649 (mt-10) REVERT: E 94 ARG cc_start: 0.7928 (mtp-110) cc_final: 0.7340 (mtm-85) REVERT: F 88 ARG cc_start: 0.7574 (ttt-90) cc_final: 0.7346 (ttt-90) REVERT: G 30 GLU cc_start: 0.8116 (mp0) cc_final: 0.7511 (tp30) REVERT: G 88 ARG cc_start: 0.7455 (mmp80) cc_final: 0.6713 (mtm110) REVERT: G 124 SER cc_start: 0.7782 (t) cc_final: 0.7485 (m) REVERT: H 68 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7536 (mttm) REVERT: H 100 GLU cc_start: 0.7310 (tt0) cc_final: 0.6812 (tm-30) REVERT: H 107 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7588 (tm-30) REVERT: I 355 MET cc_start: 0.7527 (mtt) cc_final: 0.7191 (mtt) REVERT: M 123 MET cc_start: 0.8960 (mmt) cc_final: 0.8635 (mmt) REVERT: M 167 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7268 (tm-30) REVERT: M 211 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8438 (m-30) REVERT: N 54 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8150 (m) REVERT: O 57 GLU cc_start: 0.7346 (tt0) cc_final: 0.7109 (tp30) REVERT: O 95 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7203 (mtm180) REVERT: O 222 ASP cc_start: 0.7831 (t0) cc_final: 0.7314 (p0) REVERT: O 283 MET cc_start: 0.8738 (mmm) cc_final: 0.8340 (mmt) REVERT: O 325 MET cc_start: 0.7873 (ptm) cc_final: 0.7455 (ptm) REVERT: P 82 MET cc_start: 0.8960 (tpt) cc_final: 0.8609 (tpp) REVERT: P 123 MET cc_start: 0.8758 (tpp) cc_final: 0.8271 (mmt) REVERT: P 125 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: P 165 ILE cc_start: 0.8751 (mt) cc_final: 0.8548 (mt) REVERT: P 176 MET cc_start: 0.8660 (mmp) cc_final: 0.8385 (mmm) REVERT: P 206 ARG cc_start: 0.8192 (tmm-80) cc_final: 0.7947 (ttm-80) REVERT: P 326 LYS cc_start: 0.8212 (pttp) cc_final: 0.7904 (ptmm) REVERT: Q 47 MET cc_start: 0.8214 (mmm) cc_final: 0.7285 (ptm) REVERT: Q 54 VAL cc_start: 0.9417 (OUTLIER) cc_final: 0.9208 (p) REVERT: Q 103 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8175 (p) REVERT: Q 105 LEU cc_start: 0.8294 (mt) cc_final: 0.8019 (mt) REVERT: Q 205 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7370 (mt-10) REVERT: Q 291 LYS cc_start: 0.6014 (mttm) cc_final: 0.5247 (mmtt) REVERT: Q 326 LYS cc_start: 0.8046 (pttt) cc_final: 0.7633 (mmtm) REVERT: Q 372 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7282 (ptt90) REVERT: R 75 ILE cc_start: 0.8642 (pt) cc_final: 0.8280 (pt) REVERT: R 283 MET cc_start: 0.8482 (mmm) cc_final: 0.7661 (mmp) REVERT: R 286 ASP cc_start: 0.7573 (m-30) cc_final: 0.7059 (t0) REVERT: R 291 LYS cc_start: 0.8406 (ttpp) cc_final: 0.8145 (mmtt) outliers start: 85 outliers final: 61 residues processed: 460 average time/residue: 1.1553 time to fit residues: 840.7421 Evaluate side-chains 450 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 376 time to evaluate : 4.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 173 HIS Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 176 MET Chi-restraints excluded: chain M residue 211 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain Q residue 372 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 350 SER Chi-restraints excluded: chain R residue 358 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 291 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 299 optimal weight: 3.9990 chunk 321 optimal weight: 6.9990 chunk 233 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 370 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN E 156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 39916 Z= 0.320 Angle : 0.582 7.888 54160 Z= 0.291 Chirality : 0.044 0.156 5990 Planarity : 0.004 0.058 6962 Dihedral : 8.421 159.898 5561 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.95 % Allowed : 11.60 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.12), residues: 4854 helix: -0.33 (0.12), residues: 1970 sheet: -1.13 (0.17), residues: 866 loop : 0.12 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 356 HIS 0.009 0.001 HIS E 156 PHE 0.015 0.001 PHE B 277 TYR 0.011 0.001 TYR E 133 ARG 0.007 0.000 ARG P 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 468 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 386 time to evaluate : 5.478 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: A 137 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: A 148 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7663 (mt-10) REVERT: A 276 HIS cc_start: 0.7314 (p90) cc_final: 0.6592 (p90) REVERT: A 300 SER cc_start: 0.8857 (t) cc_final: 0.8317 (p) REVERT: A 363 MET cc_start: 0.8260 (mmm) cc_final: 0.7989 (mtp) REVERT: A 406 LYS cc_start: 0.8149 (pttp) cc_final: 0.7902 (ttpp) REVERT: B 6 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7303 (mt) REVERT: B 51 ASP cc_start: 0.8336 (m-30) cc_final: 0.7679 (t0) REVERT: B 102 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6826 (ptpp) REVERT: B 224 GLU cc_start: 0.7480 (pt0) cc_final: 0.7185 (mt-10) REVERT: B 249 LYS cc_start: 0.8593 (mtmt) cc_final: 0.7964 (mtpp) REVERT: B 295 ARG cc_start: 0.7516 (mtp180) cc_final: 0.7018 (ttm170) REVERT: B 341 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: B 365 ASP cc_start: 0.8176 (t0) cc_final: 0.7826 (m-30) REVERT: C 55 ASP cc_start: 0.7476 (t0) cc_final: 0.6913 (m-30) REVERT: C 157 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6694 (p0) REVERT: C 183 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7958 (mmmm) REVERT: C 251 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7633 (mt0) REVERT: D 105 GLU cc_start: 0.7183 (tt0) cc_final: 0.6901 (tm-30) REVERT: D 206 ARG cc_start: 0.7702 (mtm-85) cc_final: 0.7302 (mtm110) REVERT: D 230 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7225 (pt0) REVERT: E 79 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6649 (mt-10) REVERT: E 94 ARG cc_start: 0.7866 (mtp-110) cc_final: 0.7261 (mtm-85) REVERT: F 88 ARG cc_start: 0.7549 (ttt-90) cc_final: 0.7343 (ttt-90) REVERT: G 30 GLU cc_start: 0.8116 (mp0) cc_final: 0.7506 (tp30) REVERT: G 88 ARG cc_start: 0.7544 (mmp80) cc_final: 0.6722 (mtm110) REVERT: G 124 SER cc_start: 0.7766 (t) cc_final: 0.7480 (m) REVERT: H 68 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7530 (mttm) REVERT: H 100 GLU cc_start: 0.7315 (tt0) cc_final: 0.7043 (tm-30) REVERT: H 107 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7576 (tm-30) REVERT: I 355 MET cc_start: 0.7556 (mtt) cc_final: 0.7219 (mtt) REVERT: M 123 MET cc_start: 0.8904 (mmt) cc_final: 0.8544 (mmt) REVERT: M 167 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7260 (tm-30) REVERT: O 57 GLU cc_start: 0.7354 (tt0) cc_final: 0.7115 (tp30) REVERT: O 95 ARG cc_start: 0.7728 (mtm110) cc_final: 0.7226 (mtm180) REVERT: O 222 ASP cc_start: 0.7818 (t0) cc_final: 0.7296 (p0) REVERT: O 283 MET cc_start: 0.8725 (mmm) cc_final: 0.8312 (mmt) REVERT: O 289 ILE cc_start: 0.8465 (pt) cc_final: 0.8073 (pt) REVERT: O 292 ASP cc_start: 0.8461 (m-30) cc_final: 0.8083 (m-30) REVERT: O 325 MET cc_start: 0.7841 (ptm) cc_final: 0.7451 (ptm) REVERT: P 82 MET cc_start: 0.8907 (tpt) cc_final: 0.8564 (tpp) REVERT: P 123 MET cc_start: 0.8801 (tpp) cc_final: 0.8340 (mmt) REVERT: P 125 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7685 (mm-30) REVERT: P 165 ILE cc_start: 0.8739 (mt) cc_final: 0.8537 (mt) REVERT: P 176 MET cc_start: 0.8670 (mmp) cc_final: 0.8432 (mmm) REVERT: P 326 LYS cc_start: 0.8228 (pttp) cc_final: 0.7913 (ptmm) REVERT: Q 47 MET cc_start: 0.8199 (mmm) cc_final: 0.7285 (ptm) REVERT: Q 54 VAL cc_start: 0.9399 (OUTLIER) cc_final: 0.9183 (p) REVERT: Q 103 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8193 (p) REVERT: Q 105 LEU cc_start: 0.8270 (mt) cc_final: 0.8068 (mt) REVERT: Q 291 LYS cc_start: 0.6004 (mttm) cc_final: 0.5230 (mmtt) REVERT: Q 326 LYS cc_start: 0.7940 (pttt) cc_final: 0.7609 (mmmm) REVERT: Q 372 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7292 (ptt90) REVERT: R 68 LYS cc_start: 0.8304 (mtpp) cc_final: 0.8086 (mtmm) REVERT: R 75 ILE cc_start: 0.8693 (pt) cc_final: 0.8332 (pt) REVERT: R 283 MET cc_start: 0.8464 (mmm) cc_final: 0.7635 (mmp) REVERT: R 286 ASP cc_start: 0.7510 (m-30) cc_final: 0.7048 (t0) REVERT: R 291 LYS cc_start: 0.8397 (ttpp) cc_final: 0.8068 (mmtt) outliers start: 82 outliers final: 60 residues processed: 450 average time/residue: 1.0928 time to fit residues: 769.7720 Evaluate side-chains 446 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 375 time to evaluate : 4.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 119 MET Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 173 HIS Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 176 MET Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 372 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 428 optimal weight: 1.9990 chunk 451 optimal weight: 2.9990 chunk 411 optimal weight: 4.9990 chunk 439 optimal weight: 3.9990 chunk 264 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 344 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 396 optimal weight: 1.9990 chunk 415 optimal weight: 4.9990 chunk 437 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS N 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 39916 Z= 0.289 Angle : 0.572 8.191 54160 Z= 0.284 Chirality : 0.044 0.154 5990 Planarity : 0.004 0.073 6962 Dihedral : 8.288 160.659 5560 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.81 % Allowed : 11.84 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.12), residues: 4854 helix: -0.28 (0.12), residues: 1980 sheet: -1.12 (0.17), residues: 866 loop : 0.18 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 356 HIS 0.009 0.001 HIS E 156 PHE 0.014 0.001 PHE B 277 TYR 0.011 0.001 TYR E 133 ARG 0.011 0.000 ARG P 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 460 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 384 time to evaluate : 4.855 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: A 137 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: A 148 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7713 (mt-10) REVERT: A 276 HIS cc_start: 0.7295 (p90) cc_final: 0.6568 (p90) REVERT: A 300 SER cc_start: 0.8863 (t) cc_final: 0.8324 (p) REVERT: A 363 MET cc_start: 0.8228 (mmm) cc_final: 0.7989 (mtp) REVERT: A 406 LYS cc_start: 0.8143 (pttp) cc_final: 0.7908 (ttpp) REVERT: B 6 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7313 (mt) REVERT: B 51 ASP cc_start: 0.8329 (m-30) cc_final: 0.7675 (t0) REVERT: B 102 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6809 (ptpp) REVERT: B 224 GLU cc_start: 0.7452 (pt0) cc_final: 0.7183 (mt-10) REVERT: B 249 LYS cc_start: 0.8584 (mtmt) cc_final: 0.7959 (mtpp) REVERT: B 295 ARG cc_start: 0.7469 (mtp180) cc_final: 0.6963 (ttm170) REVERT: B 341 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: B 365 ASP cc_start: 0.8175 (t0) cc_final: 0.7824 (m-30) REVERT: C 55 ASP cc_start: 0.7473 (t0) cc_final: 0.6909 (m-30) REVERT: C 83 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6949 (pt0) REVERT: C 157 ASN cc_start: 0.6993 (OUTLIER) cc_final: 0.6670 (p0) REVERT: C 183 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7964 (mmmm) REVERT: C 251 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7627 (mt0) REVERT: D 105 GLU cc_start: 0.7188 (tt0) cc_final: 0.6859 (tm-30) REVERT: D 206 ARG cc_start: 0.7691 (mtm-85) cc_final: 0.7313 (mtm110) REVERT: D 230 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7250 (pt0) REVERT: E 79 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6650 (mt-10) REVERT: E 94 ARG cc_start: 0.7894 (mtp-110) cc_final: 0.7266 (mtm-85) REVERT: E 170 MET cc_start: 0.8391 (mmt) cc_final: 0.7365 (mmt) REVERT: F 4 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8531 (t) REVERT: F 88 ARG cc_start: 0.7541 (ttt-90) cc_final: 0.7340 (ttt-90) REVERT: G 30 GLU cc_start: 0.8115 (mp0) cc_final: 0.7502 (tp30) REVERT: G 88 ARG cc_start: 0.7475 (mmp80) cc_final: 0.6704 (mtp85) REVERT: G 124 SER cc_start: 0.7761 (t) cc_final: 0.7480 (m) REVERT: H 68 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7400 (mttm) REVERT: H 100 GLU cc_start: 0.7314 (tt0) cc_final: 0.7038 (tm-30) REVERT: H 107 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7589 (tm-30) REVERT: I 355 MET cc_start: 0.7576 (mtt) cc_final: 0.7238 (mtt) REVERT: M 123 MET cc_start: 0.8894 (mmt) cc_final: 0.8514 (mmt) REVERT: M 167 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7263 (tm-30) REVERT: O 57 GLU cc_start: 0.7350 (tt0) cc_final: 0.7114 (tp30) REVERT: O 95 ARG cc_start: 0.7804 (mtm110) cc_final: 0.7316 (mtm180) REVERT: O 222 ASP cc_start: 0.7885 (t0) cc_final: 0.7277 (p0) REVERT: O 283 MET cc_start: 0.8715 (mmm) cc_final: 0.8298 (mmt) REVERT: O 289 ILE cc_start: 0.8459 (pt) cc_final: 0.8011 (pt) REVERT: O 292 ASP cc_start: 0.8452 (m-30) cc_final: 0.7883 (m-30) REVERT: O 325 MET cc_start: 0.7804 (ptm) cc_final: 0.7442 (ptm) REVERT: P 123 MET cc_start: 0.8796 (tpp) cc_final: 0.8344 (mmt) REVERT: P 165 ILE cc_start: 0.8727 (mt) cc_final: 0.8515 (mt) REVERT: P 176 MET cc_start: 0.8669 (mmp) cc_final: 0.8432 (mmm) REVERT: P 286 ASP cc_start: 0.7767 (m-30) cc_final: 0.7511 (t0) REVERT: P 326 LYS cc_start: 0.8239 (pttp) cc_final: 0.7919 (ptmm) REVERT: Q 47 MET cc_start: 0.8175 (mmm) cc_final: 0.7298 (ptm) REVERT: Q 54 VAL cc_start: 0.9383 (OUTLIER) cc_final: 0.9163 (p) REVERT: Q 103 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8175 (p) REVERT: Q 105 LEU cc_start: 0.8251 (mt) cc_final: 0.8040 (mt) REVERT: Q 291 LYS cc_start: 0.5905 (mttm) cc_final: 0.5095 (mmtt) REVERT: Q 326 LYS cc_start: 0.7894 (pttt) cc_final: 0.7580 (mmmm) REVERT: Q 372 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7280 (ptt90) REVERT: R 68 LYS cc_start: 0.8307 (mtpp) cc_final: 0.8030 (mtmm) REVERT: R 75 ILE cc_start: 0.8631 (pt) cc_final: 0.8352 (pt) REVERT: R 283 MET cc_start: 0.8446 (mmm) cc_final: 0.7648 (mmp) REVERT: R 286 ASP cc_start: 0.7566 (m-30) cc_final: 0.7061 (t0) REVERT: R 291 LYS cc_start: 0.8404 (ttpp) cc_final: 0.8176 (mmtt) outliers start: 76 outliers final: 60 residues processed: 442 average time/residue: 1.1616 time to fit residues: 809.3678 Evaluate side-chains 445 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 373 time to evaluate : 4.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 119 MET Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 176 MET Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 372 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 358 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 288 optimal weight: 5.9990 chunk 464 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 chunk 487 optimal weight: 4.9990 chunk 448 optimal weight: 2.9990 chunk 387 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 299 optimal weight: 0.5980 chunk 237 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS N 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39916 Z= 0.218 Angle : 0.548 6.652 54160 Z= 0.270 Chirality : 0.042 0.147 5990 Planarity : 0.004 0.070 6962 Dihedral : 8.146 161.435 5560 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.60 % Allowed : 12.24 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.12), residues: 4854 helix: -0.19 (0.12), residues: 1981 sheet: -1.04 (0.18), residues: 826 loop : 0.23 (0.14), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 356 HIS 0.008 0.001 HIS E 156 PHE 0.014 0.001 PHE M 375 TYR 0.010 0.001 TYR E 133 ARG 0.009 0.000 ARG P 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 453 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 386 time to evaluate : 4.840 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: A 276 HIS cc_start: 0.7292 (p90) cc_final: 0.6616 (p90) REVERT: A 300 SER cc_start: 0.8887 (t) cc_final: 0.8354 (p) REVERT: A 363 MET cc_start: 0.8200 (mmm) cc_final: 0.7986 (mtp) REVERT: A 406 LYS cc_start: 0.8141 (pttp) cc_final: 0.7913 (ttpp) REVERT: B 6 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7337 (mt) REVERT: B 51 ASP cc_start: 0.8334 (m-30) cc_final: 0.7698 (t0) REVERT: B 82 MET cc_start: 0.7994 (tpt) cc_final: 0.7769 (mmt) REVERT: B 224 GLU cc_start: 0.7413 (pt0) cc_final: 0.7148 (mt-10) REVERT: B 249 LYS cc_start: 0.8568 (mtmt) cc_final: 0.7947 (mtpp) REVERT: B 295 ARG cc_start: 0.7435 (mtp180) cc_final: 0.6926 (ttm170) REVERT: B 341 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: B 365 ASP cc_start: 0.8106 (t0) cc_final: 0.7874 (m-30) REVERT: C 55 ASP cc_start: 0.7457 (t0) cc_final: 0.6896 (m-30) REVERT: C 83 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7003 (pt0) REVERT: C 157 ASN cc_start: 0.6867 (OUTLIER) cc_final: 0.6517 (p0) REVERT: C 183 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7961 (mmmm) REVERT: C 251 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7628 (mt0) REVERT: D 105 GLU cc_start: 0.7173 (tt0) cc_final: 0.6830 (tm-30) REVERT: D 206 ARG cc_start: 0.7678 (mtm-85) cc_final: 0.7291 (mtm110) REVERT: D 230 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7261 (pt0) REVERT: E 79 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6642 (mt-10) REVERT: E 94 ARG cc_start: 0.7870 (mtp-110) cc_final: 0.7247 (mtm-85) REVERT: E 170 MET cc_start: 0.8434 (mmt) cc_final: 0.7386 (mmt) REVERT: F 4 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8519 (t) REVERT: F 88 ARG cc_start: 0.7529 (ttt-90) cc_final: 0.7277 (ttt-90) REVERT: G 30 GLU cc_start: 0.8110 (mp0) cc_final: 0.7494 (tp30) REVERT: G 88 ARG cc_start: 0.7264 (mmp80) cc_final: 0.6227 (mtp85) REVERT: G 124 SER cc_start: 0.7736 (t) cc_final: 0.7467 (m) REVERT: H 68 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7354 (mttm) REVERT: H 100 GLU cc_start: 0.7312 (tt0) cc_final: 0.7038 (tm-30) REVERT: H 107 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7490 (tm-30) REVERT: I 355 MET cc_start: 0.7577 (mtt) cc_final: 0.7234 (mtt) REVERT: M 123 MET cc_start: 0.8892 (mmt) cc_final: 0.8509 (mmt) REVERT: M 167 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7201 (tm-30) REVERT: O 57 GLU cc_start: 0.7336 (tt0) cc_final: 0.7115 (tp30) REVERT: O 95 ARG cc_start: 0.7799 (mtm110) cc_final: 0.7310 (mtm180) REVERT: O 222 ASP cc_start: 0.7786 (t0) cc_final: 0.7104 (p0) REVERT: O 283 MET cc_start: 0.8701 (mmm) cc_final: 0.8276 (mmt) REVERT: O 289 ILE cc_start: 0.8445 (pt) cc_final: 0.8045 (pt) REVERT: O 292 ASP cc_start: 0.8441 (m-30) cc_final: 0.8062 (m-30) REVERT: O 325 MET cc_start: 0.7770 (ptm) cc_final: 0.7401 (ptm) REVERT: P 82 MET cc_start: 0.8913 (tpt) cc_final: 0.8542 (tpp) REVERT: P 123 MET cc_start: 0.8793 (tpp) cc_final: 0.8348 (mmt) REVERT: P 125 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7475 (mm-30) REVERT: P 165 ILE cc_start: 0.8713 (mt) cc_final: 0.8490 (mt) REVERT: P 176 MET cc_start: 0.8658 (mmp) cc_final: 0.8419 (mmm) REVERT: P 326 LYS cc_start: 0.8228 (pttp) cc_final: 0.7904 (ptmm) REVERT: Q 47 MET cc_start: 0.8120 (mmm) cc_final: 0.7270 (ptm) REVERT: Q 103 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8184 (p) REVERT: Q 105 LEU cc_start: 0.8280 (mt) cc_final: 0.8079 (mt) REVERT: Q 291 LYS cc_start: 0.5890 (mttm) cc_final: 0.5183 (mmtt) REVERT: Q 326 LYS cc_start: 0.7904 (pttt) cc_final: 0.7581 (mmmm) REVERT: Q 328 LYS cc_start: 0.7437 (ttmm) cc_final: 0.6953 (tptt) REVERT: Q 372 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7277 (ptt90) REVERT: R 68 LYS cc_start: 0.8307 (mtpp) cc_final: 0.8029 (mtmm) REVERT: R 75 ILE cc_start: 0.8615 (pt) cc_final: 0.8328 (pt) REVERT: R 283 MET cc_start: 0.8448 (mmm) cc_final: 0.7658 (mmp) REVERT: R 286 ASP cc_start: 0.7547 (m-30) cc_final: 0.7041 (t0) REVERT: R 291 LYS cc_start: 0.8394 (ttpp) cc_final: 0.8175 (mmtt) outliers start: 67 outliers final: 54 residues processed: 437 average time/residue: 1.1246 time to fit residues: 765.0599 Evaluate side-chains 443 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 379 time to evaluate : 4.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 119 MET Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 372 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 308 optimal weight: 6.9990 chunk 413 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 357 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 388 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 398 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS N 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.121365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.097816 restraints weight = 177756.977| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.88 r_work: 0.3105 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.387 39916 Z= 0.274 Angle : 0.639 59.175 54160 Z= 0.353 Chirality : 0.042 0.243 5990 Planarity : 0.004 0.068 6962 Dihedral : 8.141 161.498 5557 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.62 % Allowed : 12.29 % Favored : 86.09 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.12), residues: 4854 helix: -0.18 (0.12), residues: 1981 sheet: -1.04 (0.18), residues: 826 loop : 0.24 (0.14), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 356 HIS 0.008 0.001 HIS E 156 PHE 0.013 0.001 PHE B 277 TYR 0.011 0.001 TYR E 133 ARG 0.007 0.000 ARG P 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16129.49 seconds wall clock time: 280 minutes 31.40 seconds (16831.40 seconds total)