Starting phenix.real_space_refine on Sun Mar 17 04:01:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxw_42787/03_2024/8uxw_42787_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxw_42787/03_2024/8uxw_42787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxw_42787/03_2024/8uxw_42787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxw_42787/03_2024/8uxw_42787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxw_42787/03_2024/8uxw_42787_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxw_42787/03_2024/8uxw_42787_trim_updated.pdb" } resolution = 2.7 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= 0.002 sd= 0.090 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: 7 Type Number sf(0) Gaussians P 21 5.49 5 Mg 10 5.21 5 S 230 5.16 5 C 24684 2.51 5 N 6643 2.21 5 O 7441 1.98 5 H 38258 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 TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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 TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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 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 TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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 GLU 226": "OE1" <-> "OE2" Residue "P ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ASP 288": "OD1" <-> "OD2" 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 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 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 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 77287 Number of models: 1 Model: "" Number of chains: 25 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: 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: "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: 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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} Time building chain proxies: 24.74, per 1000 atoms: 0.32 Number of scatterers: 77287 At special positions: 0 Unit cell: (129.216, 205.938, 227.474, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 230 16.00 P 21 15.00 Mg 10 11.99 O 7441 8.00 N 6643 7.00 C 24684 6.00 H 38258 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=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 49.25 Conformation dependent library (CDL) restraints added in 5.9 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: 221 helices and 53 sheets defined 41.5% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.10 Creating SS restraints... Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.580A pdb=" N LYS A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA A 86 " --> pdb=" O LYS A 82 " (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 147 Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.542A pdb=" N ALA A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 168 " --> pdb=" O ALA A 164 " (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 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: 3.723A pdb=" N LEU A 288 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 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: 4.996A pdb=" N LYS A 324 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 328 " --> pdb=" O GLY A 325 " (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 removed outlier: 3.715A pdb=" N SER A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 removed outlier: 3.677A pdb=" N ALA A 385 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 386 " --> pdb=" O ARG A 383 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 388 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 389 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 391 " --> pdb=" O PHE A 388 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 393 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 394 " --> pdb=" O SER A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 402 No H-bonds generated for 'chain 'A' and resid 399 through 402' Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.585A pdb=" N GLU A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ALA A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N SER A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE A 416 " --> pdb=" O TYR A 412 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 64 removed outlier: 3.896A pdb=" N VAL B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N SER B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.550A pdb=" N GLN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.665A pdb=" N LYS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.757A pdb=" N PHE B 206 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU B 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 209 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 214 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.653A pdb=" N GLU B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.893A pdb=" N LYS B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYR B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.613A 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 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: 5.289A pdb=" N VAL B 350 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 352 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 355 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA B 358 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 384 removed outlier: 3.731A pdb=" N GLU B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N VAL B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ARG B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 4.934A 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: 3.660A pdb=" N SER D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 65 removed outlier: 3.604A pdb=" N ASN D 64 " --> pdb=" O PRO D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 78 removed outlier: 7.379A pdb=" N ALA D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 7.454A 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 139 removed outlier: 4.091A pdb=" N ALA D 121 " --> pdb=" O ASN D 117 " (cutoff:3.500A) Proline residue: D 122 - end of helix Processing helix chain 'D' and resid 144 through 154 removed outlier: 3.992A pdb=" N SER D 153 " --> pdb=" O LYS D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 205 removed outlier: 3.848A pdb=" N VAL D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG D 205 " --> pdb=" O VAL D 201 " (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 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 255 through 263 Processing helix chain 'D' and resid 265 through 298 removed outlier: 3.872A pdb=" N LYS D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA D 278 " --> pdb=" O LYS D 274 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG D 287 " --> pdb=" O ARG D 283 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 4.478A 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 56 removed outlier: 4.386A pdb=" N ARG E 52 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA E 53 " --> pdb=" O GLY E 49 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 83 Processing helix chain 'E' and resid 89 through 101 Processing helix chain 'E' and resid 126 through 149 removed outlier: 3.749A pdb=" N SER E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS E 148 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 166 removed outlier: 5.970A pdb=" N PHE E 164 " --> pdb=" O TRP E 160 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER E 165 " --> pdb=" O TRP E 161 " (cutoff:3.500A) removed outlier: 4.964A 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 Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 128 through 167 removed outlier: 5.007A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ALA F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.931A 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 Proline residue: G 41 - end of helix removed outlier: 3.607A pdb=" N ILE G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 61 removed outlier: 3.813A pdb=" N SER G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 86 Processing helix chain 'G' and resid 92 through 98 removed outlier: 3.936A pdb=" N GLU G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 Processing helix chain 'G' and resid 123 through 137 Processing helix chain 'G' and resid 139 through 147 removed outlier: 3.556A pdb=" N ARG G 144 " --> pdb=" O CYS G 141 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN G 147 " --> pdb=" O ARG G 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 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: 3.892A 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 removed outlier: 3.568A pdb=" N MET H 123 " --> pdb=" O MET H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 145 removed outlier: 3.580A pdb=" N SER H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 182 through 196 removed outlier: 3.999A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) removed outlier: 4.216A 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 262 removed outlier: 3.734A pdb=" N ARG H 256 " --> pdb=" O GLU H 253 " (cutoff:3.500A) removed outlier: 4.757A 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 283 Processing helix chain 'H' and resid 287 through 290 No H-bonds generated for 'chain 'H' and resid 287 through 290' Processing helix chain 'H' and resid 293 through 295 No H-bonds generated for 'chain 'H' and resid 293 through 295' Processing helix chain 'H' and resid 302 through 305 Processing helix chain 'H' and resid 309 through 320 removed outlier: 3.693A pdb=" N ALA H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 348 removed outlier: 5.646A pdb=" N VAL H 339 " --> pdb=" O LYS H 336 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY H 342 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA H 347 " --> pdb=" O SER H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 365 Processing helix chain 'H' and resid 367 through 373 removed outlier: 3.582A pdb=" N VAL H 370 " --> pdb=" O PRO H 367 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS H 373 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 64 removed outlier: 5.842A pdb=" N GLY I 63 " --> pdb=" O GLN I 59 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE I 64 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 91 removed outlier: 4.047A pdb=" N LYS I 84 " --> pdb=" O ASP I 80 " (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: 3.740A pdb=" N MET I 123 " --> pdb=" O MET I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 142 Processing helix chain 'I' and resid 182 through 196 removed outlier: 3.713A pdb=" N THR I 194 " --> pdb=" O MET I 190 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU I 195 " --> pdb=" O LYS I 191 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG I 196 " --> pdb=" O ILE I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 216 removed outlier: 3.789A pdb=" N GLU I 207 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 232 Processing helix chain 'I' and resid 252 through 261 removed outlier: 3.641A pdb=" N ARG I 256 " --> pdb=" O GLU I 253 " (cutoff:3.500A) removed outlier: 4.765A 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 Processing helix chain 'I' and resid 289 through 295 removed outlier: 4.260A pdb=" N ASP I 292 " --> pdb=" O ILE I 289 " (cutoff:3.500A) removed outlier: 5.536A 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 338 through 348 Processing helix chain 'I' and resid 359 through 372 removed outlier: 5.688A pdb=" N GLU I 364 " --> pdb=" O GLN I 360 " (cutoff:3.500A) Proline residue: I 367 - end of helix removed outlier: 5.202A pdb=" N VAL I 370 " --> pdb=" O GLY I 366 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N HIS I 371 " --> pdb=" O PRO I 367 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 60 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: 3.670A pdb=" N MET M 123 " --> pdb=" O MET M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 145 Processing helix chain 'M' and resid 182 through 196 removed outlier: 4.306A pdb=" N THR M 194 " --> pdb=" O MET M 190 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU M 195 " --> pdb=" O LYS M 191 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG M 196 " --> pdb=" O ILE M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 213 Processing helix chain 'M' and resid 223 through 230 Processing helix chain 'M' and resid 252 through 261 removed outlier: 3.694A pdb=" N ARG M 256 " --> pdb=" O GLU M 253 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N CYS M 257 " --> pdb=" O ARG M 254 " (cutoff:3.500A) Proline residue: M 258 - end of helix Processing helix chain 'M' and resid 264 through 267 Processing helix chain 'M' and resid 274 through 284 Processing helix chain 'M' and resid 290 through 294 Processing helix chain 'M' and resid 302 through 305 Processing helix chain 'M' and resid 309 through 320 Processing helix chain 'M' and resid 338 through 348 Processing helix chain 'M' and resid 350 through 354 removed outlier: 3.592A pdb=" N GLN M 353 " --> pdb=" O SER M 350 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN M 354 " --> pdb=" O THR M 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 350 through 354' Processing helix chain 'M' and resid 359 through 365 removed outlier: 5.690A pdb=" N GLU M 364 " --> pdb=" O GLN M 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 373 removed outlier: 3.570A pdb=" N LYS M 373 " --> pdb=" O VAL M 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 61 removed outlier: 3.568A pdb=" N LYS N 61 " --> pdb=" O GLU N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 91 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: 3.649A pdb=" N SER N 141 " --> pdb=" O GLN N 137 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR N 143 " --> pdb=" O VAL N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 182 through 196 removed outlier: 3.568A pdb=" N THR N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU N 195 " --> pdb=" O LYS N 191 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG N 196 " --> pdb=" O ILE N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 216 removed outlier: 4.213A pdb=" N LYS N 215 " --> pdb=" O ASP N 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 231 removed outlier: 3.547A pdb=" N ALA N 231 " --> pdb=" O MET N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 262 removed outlier: 4.091A pdb=" N ARG N 256 " --> pdb=" O GLU N 253 " (cutoff:3.500A) removed outlier: 4.528A 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 294 Processing helix chain 'N' and resid 302 through 304 No H-bonds generated for 'chain 'N' and resid 302 through 304' Processing helix chain 'N' and resid 309 through 320 Processing helix chain 'N' and resid 338 through 346 Processing helix chain 'N' and resid 359 through 365 removed outlier: 3.677A pdb=" N GLU N 364 " --> pdb=" O GLN N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 367 through 373 removed outlier: 3.547A pdb=" N LYS N 373 " --> pdb=" O VAL N 370 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 64 removed outlier: 5.891A pdb=" N GLY O 63 " --> pdb=" O GLN O 59 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE O 64 " --> pdb=" O SER O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 91 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 Processing helix chain 'O' and resid 137 through 145 removed outlier: 3.581A pdb=" N TYR O 143 " --> pdb=" O VAL O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 196 removed outlier: 4.204A pdb=" N GLU O 195 " --> pdb=" O LYS O 191 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG O 196 " --> pdb=" O ILE O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 205 through 216 removed outlier: 3.565A pdb=" N LYS O 215 " --> pdb=" O ASP O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 231 Processing helix chain 'O' and resid 252 through 261 removed outlier: 3.793A pdb=" N ARG O 256 " --> pdb=" O GLU O 253 " (cutoff:3.500A) removed outlier: 4.863A 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 290 through 296 Processing helix chain 'O' and resid 302 through 304 No H-bonds generated for 'chain 'O' and resid 302 through 304' Processing helix chain 'O' and resid 309 through 320 Processing helix chain 'O' and resid 335 through 348 removed outlier: 3.563A pdb=" N SER O 338 " --> pdb=" O ARG O 335 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL O 339 " --> pdb=" O LYS O 336 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY O 342 " --> pdb=" O VAL O 339 " (cutoff:3.500A) removed outlier: 4.002A 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 370 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 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 removed outlier: 3.519A pdb=" N MET P 123 " --> pdb=" O MET P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 144 Processing helix chain 'P' and resid 182 through 194 removed outlier: 3.563A pdb=" N THR P 194 " --> pdb=" O MET P 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 216 removed outlier: 3.581A pdb=" N GLU P 207 " --> pdb=" O THR P 203 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 232 Processing helix chain 'P' and resid 252 through 261 removed outlier: 3.914A pdb=" N ARG P 256 " --> pdb=" O GLU P 253 " (cutoff:3.500A) removed outlier: 4.915A 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 290 through 296 Processing helix chain 'P' and resid 302 through 304 No H-bonds generated for 'chain 'P' and resid 302 through 304' Processing helix chain 'P' and resid 309 through 320 Processing helix chain 'P' and resid 338 through 348 Processing helix chain 'P' and resid 359 through 365 removed outlier: 3.794A pdb=" N GLU P 364 " --> pdb=" O GLN P 360 " (cutoff:3.500A) Processing helix chain 'P' and resid 367 through 373 removed outlier: 3.543A pdb=" N LYS P 373 " --> pdb=" O VAL P 370 " (cutoff:3.500A) 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 Processing helix chain 'Q' and resid 113 through 125 Processing helix chain 'Q' and resid 137 through 145 Processing helix chain 'Q' and resid 182 through 196 removed outlier: 4.020A pdb=" N GLU Q 195 " --> pdb=" O LYS Q 191 " (cutoff:3.500A) removed outlier: 4.180A 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 232 Processing helix chain 'Q' and resid 234 through 236 No H-bonds generated for 'chain 'Q' and resid 234 through 236' Processing helix chain 'Q' and resid 252 through 256 removed outlier: 4.040A 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: 4.531A pdb=" N LYS Q 291 " --> pdb=" O ILE Q 287 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP Q 292 " --> pdb=" O ASP Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 304 No H-bonds generated for 'chain 'Q' and resid 302 through 304' Processing helix chain 'Q' and resid 309 through 320 Processing helix chain 'Q' and resid 335 through 348 removed outlier: 5.770A pdb=" N VAL Q 339 " --> pdb=" O LYS Q 336 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA Q 347 " --> pdb=" O SER Q 344 " (cutoff:3.500A) Processing helix chain 'Q' and resid 350 through 352 No H-bonds generated for 'chain 'Q' and resid 350 through 352' Processing helix chain 'Q' and resid 359 through 362 No H-bonds generated for 'chain 'Q' and resid 359 through 362' Processing helix chain 'Q' and resid 367 through 373 removed outlier: 3.763A pdb=" N LYS Q 373 " --> pdb=" O VAL Q 370 " (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 Processing helix chain 'R' and resid 98 through 100 No H-bonds generated for 'chain 'R' and resid 98 through 100' Processing helix chain 'R' and resid 113 through 125 Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.729A pdb=" N SER R 141 " --> pdb=" O GLN R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 196 removed outlier: 4.371A pdb=" N GLU R 195 " --> pdb=" O LYS R 191 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG R 196 " --> pdb=" O ILE R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 216 removed outlier: 3.957A pdb=" N GLU R 207 " --> pdb=" O THR R 203 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE R 208 " --> pdb=" O ALA R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 235 removed outlier: 3.907A pdb=" N SER R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER R 233 " --> pdb=" O THR R 229 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N SER R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N SER R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 261 removed outlier: 3.947A pdb=" N ARG R 256 " --> pdb=" O GLU R 253 " (cutoff:3.500A) removed outlier: 4.797A 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 283 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 318 Processing helix chain 'R' and resid 338 through 348 Processing helix chain 'R' and resid 359 through 363 Processing helix chain 'R' and resid 367 through 370 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 12 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 125 through 130 removed outlier: 6.731A pdb=" N GLY A 154 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU A 128 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR A 156 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLU A 130 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA A 158 " --> pdb=" O GLU A 130 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 330 through 333 removed outlier: 6.556A pdb=" N THR A 182 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N SER A 333 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL A 184 " --> pdb=" O SER A 333 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 266 through 271 Processing sheet with id= F, first strand: chain 'B' and resid 131 through 136 removed outlier: 6.754A pdb=" N ILE B 6 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N THR B 106 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEU B 8 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 33 through 36 Processing sheet with id= H, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.599A pdb=" N VAL B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N SER B 300 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= J, first strand: chain 'C' and resid 16 through 19 removed outlier: 4.546A pdb=" N GLU C 16 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG C 49 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU C 39 " --> pdb=" O HIS C 47 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N HIS C 47 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ASP C 41 " --> pdb=" O TRP C 45 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TRP C 45 " --> pdb=" O ASP C 41 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 90 through 95 removed outlier: 3.805A pdb=" N ALA C 79 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG C 69 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS C 60 " --> pdb=" O CYS C 73 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 135 through 141 removed outlier: 3.505A pdb=" N TRP C 135 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE C 105 " --> pdb=" O GLY C 118 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 149 through 154 removed outlier: 6.601A pdb=" N GLY C 164 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU C 152 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA C 162 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TRP C 154 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU C 160 " --> pdb=" O TRP C 154 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS C 169 " --> pdb=" O CYS C 165 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER C 174 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 198 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 243 through 248 removed outlier: 3.661A pdb=" N ALA C 243 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 254 through 259 removed outlier: 6.831A pdb=" N ALA C 268 " --> pdb=" O ARG C 255 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU C 257 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 266 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TRP C 259 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ALA C 264 " --> pdb=" O TRP C 259 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN C 278 " --> pdb=" O HIS C 286 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N HIS C 286 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASN C 280 " --> pdb=" O TRP C 284 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TRP C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 3 through 9 removed outlier: 6.803A 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) removed outlier: 3.535A pdb=" N THR C 349 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 28 through 32 Processing sheet with id= R, first strand: chain 'D' and resid 157 through 159 Processing sheet with id= S, first strand: chain 'F' and resid 114 through 119 removed outlier: 3.531A pdb=" N ILE F 114 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN F 56 " --> pdb=" O GLU F 59 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N CYS F 61 " --> pdb=" O SER F 54 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N SER F 54 " --> pdb=" O CYS F 61 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE F 63 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N VAL F 52 " --> pdb=" O ILE F 63 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.719A pdb=" N THR H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ALA H 135 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 35 through 38 Processing sheet with id= V, first strand: chain 'H' and resid 297 through 300 removed outlier: 6.291A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N SER H 300 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU H 153 " --> pdb=" O SER H 300 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 238 through 241 Processing sheet with id= X, first strand: chain 'I' and resid 29 through 32 removed outlier: 8.143A pdb=" N CYS I 10 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU I 104 " --> pdb=" O CYS I 10 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 52 through 54 Processing sheet with id= Z, first strand: chain 'I' and resid 297 through 300 removed outlier: 6.566A pdb=" N ILE I 151 " --> pdb=" O VAL I 298 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N SER I 300 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU I 153 " --> pdb=" O SER I 300 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 238 through 241 Processing sheet with id= AB, first strand: chain 'M' and resid 132 through 136 removed outlier: 6.769A pdb=" N THR M 103 " --> pdb=" O TYR M 133 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ALA M 135 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU M 105 " --> pdb=" O ALA M 135 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU M 8 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N THR M 106 " --> pdb=" O LEU M 8 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N CYS M 10 " --> pdb=" O THR M 106 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'M' and resid 35 through 38 Processing sheet with id= AD, first strand: chain 'M' and resid 297 through 300 removed outlier: 6.513A pdb=" N ILE M 151 " --> pdb=" O VAL M 298 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER M 300 " --> pdb=" O ILE M 151 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU M 153 " --> pdb=" O SER M 300 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 238 through 241 Processing sheet with id= AF, first strand: chain 'N' and resid 132 through 136 removed outlier: 6.809A pdb=" N THR N 103 " --> pdb=" O TYR N 133 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA N 135 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU N 105 " --> pdb=" O ALA N 135 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU N 8 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N THR N 106 " --> pdb=" O LEU N 8 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N CYS N 10 " --> pdb=" O THR N 106 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 35 through 38 Processing sheet with id= AH, first strand: chain 'N' and resid 297 through 300 removed outlier: 6.395A pdb=" N ILE N 151 " --> pdb=" O VAL N 298 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N SER N 300 " --> pdb=" O ILE N 151 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU N 153 " --> pdb=" O SER N 300 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 238 through 241 Processing sheet with id= AJ, first strand: chain 'O' and resid 132 through 136 removed outlier: 6.681A pdb=" N THR O 103 " --> pdb=" O TYR O 133 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ALA O 135 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU O 105 " --> pdb=" O ALA O 135 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU O 8 " --> pdb=" O LEU O 104 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N THR O 106 " --> pdb=" O LEU O 8 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N CYS O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'O' and resid 35 through 38 Processing sheet with id= AL, first strand: chain 'O' and resid 297 through 300 removed outlier: 6.521A pdb=" N ILE O 151 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N SER O 300 " --> pdb=" O ILE O 151 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU O 153 " --> pdb=" O SER O 300 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'O' and resid 238 through 241 Processing sheet with id= AN, first strand: chain 'P' and resid 132 through 136 removed outlier: 6.801A pdb=" N THR P 103 " --> pdb=" O TYR P 133 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA P 135 " --> pdb=" O THR P 103 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU P 105 " --> pdb=" O ALA P 135 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU P 8 " --> pdb=" O LEU P 104 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N THR P 106 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N CYS P 10 " --> pdb=" O THR P 106 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'P' and resid 35 through 38 Processing sheet with id= AP, first strand: chain 'P' and resid 297 through 300 removed outlier: 6.260A pdb=" N ILE P 151 " --> pdb=" O VAL P 298 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N SER P 300 " --> pdb=" O ILE P 151 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU P 153 " --> pdb=" O SER P 300 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'P' and resid 238 through 241 Processing sheet with id= AR, first strand: chain 'Q' and resid 8 through 12 Processing sheet with id= AS, first strand: chain 'Q' and resid 35 through 38 Processing sheet with id= AT, first strand: chain 'Q' and resid 103 through 107 Processing sheet with id= AU, first strand: chain 'Q' and resid 297 through 300 removed outlier: 6.371A pdb=" N ILE Q 151 " --> pdb=" O VAL Q 298 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N SER Q 300 " --> pdb=" O ILE Q 151 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU Q 153 " --> pdb=" O SER Q 300 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Q' and resid 238 through 241 Processing sheet with id= AW, first strand: chain 'R' and resid 8 through 12 Processing sheet with id= AX, first strand: chain 'R' and resid 35 through 38 Processing sheet with id= AY, first strand: chain 'R' and resid 103 through 107 Processing sheet with id= AZ, first strand: chain 'R' and resid 297 through 300 removed outlier: 6.519A pdb=" N ILE R 151 " --> pdb=" O VAL R 298 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N SER R 300 " --> pdb=" O ILE R 151 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU R 153 " --> pdb=" O SER R 300 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'R' and resid 238 through 241 1447 hydrogen bonds defined for protein. 3804 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: 34.08 Time building geometry restraints manager: 51.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.77 - 0.98: 846 0.98 - 1.19: 37349 1.19 - 1.40: 14272 1.40 - 1.61: 25290 1.61 - 1.82: 396 Bond restraints: 78153 Sorted by residual: bond pdb=" NH2 ARG I 210 " pdb="HH21 ARG I 210 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N THR P 278 " pdb=" H THR P 278 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH2 ARG D 162 " pdb="HH22 ARG D 162 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE1 TYR B 143 " pdb=" HE1 TYR B 143 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N GLU Q 107 " pdb=" H GLU Q 107 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 78148 not shown) Histogram of bond angle deviations from ideal: 93.93 - 102.19: 281 102.19 - 110.45: 73736 110.45 - 118.71: 34364 118.71 - 126.97: 32103 126.97 - 135.23: 642 Bond angle restraints: 141126 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 136.83 121.93 14.90 1.00e+00 1.00e+00 2.22e+02 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 125.32 14.55 1.00e+00 1.00e+00 2.12e+02 angle pdb=" O2B ADP M 802 " pdb=" PB ADP M 802 " pdb=" O3B ADP M 802 " ideal model delta sigma weight residual 119.90 96.84 23.06 3.00e+00 1.11e-01 5.91e+01 angle pdb=" O1B ADP I 802 " pdb=" PB ADP I 802 " pdb=" O2B ADP I 802 " ideal model delta sigma weight residual 119.90 96.90 23.00 3.00e+00 1.11e-01 5.88e+01 angle pdb=" O1B ADP P 802 " pdb=" PB ADP P 802 " pdb=" O3B ADP P 802 " ideal model delta sigma weight residual 119.90 97.12 22.78 3.00e+00 1.11e-01 5.77e+01 ... (remaining 141121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.11: 35087 31.11 - 62.22: 1563 62.22 - 93.33: 250 93.33 - 124.44: 8 124.44 - 155.54: 8 Dihedral angle restraints: 36916 sinusoidal: 20203 harmonic: 16713 Sorted by residual: dihedral pdb=" O1B ADP M 802 " pdb=" O3A ADP M 802 " pdb=" PB ADP M 802 " pdb=" PA ADP M 802 " ideal model delta sinusoidal sigma weight residual -60.00 95.54 -155.54 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP Q 802 " pdb=" O3A ADP Q 802 " pdb=" PA ADP Q 802 " pdb=" PB ADP Q 802 " ideal model delta sinusoidal sigma weight residual -60.00 93.12 -153.12 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" O1B ADP R 802 " pdb=" O3A ADP R 802 " pdb=" PB ADP R 802 " pdb=" PA ADP R 802 " ideal model delta sinusoidal sigma weight residual -60.00 92.18 -152.19 1 2.00e+01 2.50e-03 4.52e+01 ... (remaining 36913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4674 0.123 - 0.245: 1174 0.245 - 0.368: 130 0.368 - 0.491: 10 0.491 - 0.613: 2 Chirality restraints: 5990 Sorted by residual: chirality pdb=" CA ARG D 287 " pdb=" N ARG D 287 " pdb=" C ARG D 287 " pdb=" CB ARG D 287 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.40e+00 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 1.96 0.55 2.00e-01 2.50e+01 7.51e+00 chirality pdb=" CA CYS F 167 " pdb=" N CYS F 167 " pdb=" C CYS F 167 " pdb=" CB CYS F 167 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.94e+00 ... (remaining 5987 not shown) Planarity restraints: 11601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP O 340 " 0.324 2.00e-02 2.50e+03 1.21e-01 5.89e+02 pdb=" CG TRP O 340 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP O 340 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP O 340 " -0.124 2.00e-02 2.50e+03 pdb=" NE1 TRP O 340 " -0.135 2.00e-02 2.50e+03 pdb=" CE2 TRP O 340 " -0.098 2.00e-02 2.50e+03 pdb=" CE3 TRP O 340 " -0.112 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 340 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 340 " -0.032 2.00e-02 2.50e+03 pdb=" CH2 TRP O 340 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 TRP O 340 " 0.087 2.00e-02 2.50e+03 pdb=" HE1 TRP O 340 " -0.059 2.00e-02 2.50e+03 pdb=" HE3 TRP O 340 " -0.126 2.00e-02 2.50e+03 pdb=" HZ2 TRP O 340 " 0.110 2.00e-02 2.50e+03 pdb=" HZ3 TRP O 340 " 0.008 2.00e-02 2.50e+03 pdb=" HH2 TRP O 340 " 0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 340 " 0.335 2.00e-02 2.50e+03 1.21e-01 5.81e+02 pdb=" CG TRP M 340 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP M 340 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP M 340 " -0.105 2.00e-02 2.50e+03 pdb=" NE1 TRP M 340 " -0.137 2.00e-02 2.50e+03 pdb=" CE2 TRP M 340 " -0.081 2.00e-02 2.50e+03 pdb=" CE3 TRP M 340 " -0.113 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 340 " 0.026 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 340 " -0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP M 340 " 0.053 2.00e-02 2.50e+03 pdb=" HD1 TRP M 340 " 0.054 2.00e-02 2.50e+03 pdb=" HE1 TRP M 340 " -0.062 2.00e-02 2.50e+03 pdb=" HE3 TRP M 340 " -0.139 2.00e-02 2.50e+03 pdb=" HZ2 TRP M 340 " 0.118 2.00e-02 2.50e+03 pdb=" HZ3 TRP M 340 " -0.004 2.00e-02 2.50e+03 pdb=" HH2 TRP M 340 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 387 " 0.309 2.00e-02 2.50e+03 1.18e-01 5.60e+02 pdb=" CG TRP A 387 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 387 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 387 " -0.062 2.00e-02 2.50e+03 pdb=" NE1 TRP A 387 " -0.130 2.00e-02 2.50e+03 pdb=" CE2 TRP A 387 " -0.044 2.00e-02 2.50e+03 pdb=" CE3 TRP A 387 " -0.097 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 387 " 0.052 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 387 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP A 387 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 TRP A 387 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 TRP A 387 " -0.144 2.00e-02 2.50e+03 pdb=" HE3 TRP A 387 " -0.165 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 387 " 0.119 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 387 " -0.046 2.00e-02 2.50e+03 pdb=" HH2 TRP A 387 " 0.140 2.00e-02 2.50e+03 ... (remaining 11598 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 5185 2.17 - 2.78: 134262 2.78 - 3.38: 231379 3.38 - 3.99: 315187 3.99 - 4.60: 457679 Nonbonded interactions: 1143692 Sorted by model distance: nonbonded pdb=" HG SER B 275 " pdb=" OE1 GLU B 316 " model vdw 1.560 1.850 nonbonded pdb=" OD1 ASP C 328 " pdb=" HG1 THR O 351 " model vdw 1.584 1.850 nonbonded pdb=" HG SER B 311 " pdb=" OE1 GLU F 31 " model vdw 1.587 1.850 nonbonded pdb=" OE2 GLU A 106 " pdb=" HG SER A 149 " model vdw 1.590 1.850 nonbonded pdb=" OE1 GLU O 270 " pdb=" HG1 THR P 202 " model vdw 1.595 1.850 ... (remaining 1143687 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 or resid 801 through 802)) 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 or resid 801 through 802)) 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 or resid 801 through 802)) selection = chain 'N' 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 or resid 801 through 802)) 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 or resid 801 through 802)) 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 or resid 801 through 802)) 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 or resid 801 through 802)) } 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: 5.700 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: 0.840 Extract box with map and model: 28.030 Check model and map are aligned: 0.820 Set scattering table: 0.540 Process input model: 198.200 Find NCS groups from input model: 3.180 Set up NCS constraints: 0.450 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: 0.030 Load rotamer database and sin/cos tables:14.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 252.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.141 39895 Z= 0.842 Angle : 1.916 23.059 54139 Z= 1.259 Chirality : 0.104 0.613 5990 Planarity : 0.017 0.387 6962 Dihedral : 15.354 155.545 14846 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.99 % Favored : 96.99 % Rotamer: Outliers : 2.69 % Allowed : 5.81 % Favored : 91.50 % Cbeta Deviations : 0.33 % 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: -1.20 (0.11), residues: 4854 helix: -1.74 (0.10), residues: 1937 sheet: -0.26 (0.19), residues: 627 loop : 0.18 (0.12), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.222 0.031 TRP M 340 HIS 0.016 0.004 HIS Q 371 PHE 0.117 0.013 PHE F 101 TYR 0.176 0.018 TYR B 127 ARG 0.017 0.002 ARG F 156 *********************** 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 1217 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1104 time to evaluate : 4.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.6906 (mtt-85) cc_final: 0.6021 (mtm180) REVERT: A 226 ASP cc_start: 0.7315 (m-30) cc_final: 0.6885 (m-30) REVERT: A 228 ASN cc_start: 0.7081 (OUTLIER) cc_final: 0.6766 (m-40) REVERT: A 235 LYS cc_start: 0.6483 (pttp) cc_final: 0.6270 (ptmt) REVERT: A 239 ARG cc_start: 0.6322 (mtt180) cc_final: 0.5822 (mtm-85) REVERT: A 253 LYS cc_start: 0.6842 (mppt) cc_final: 0.6306 (mptt) REVERT: A 297 GLU cc_start: 0.6379 (mt-10) cc_final: 0.5385 (mp0) REVERT: A 340 LYS cc_start: 0.7326 (tptp) cc_final: 0.6684 (tttt) REVERT: A 406 LYS cc_start: 0.7013 (pttp) cc_final: 0.6740 (ptpp) REVERT: B 6 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7337 (mt) REVERT: B 21 LYS cc_start: 0.8463 (mtmt) cc_final: 0.7882 (mtmm) REVERT: B 68 LYS cc_start: 0.6426 (mtmt) cc_final: 0.6012 (mtmt) REVERT: B 72 GLU cc_start: 0.7770 (tt0) cc_final: 0.7441 (tt0) REVERT: B 73 ASN cc_start: 0.7177 (m-40) cc_final: 0.6589 (t0) REVERT: B 96 ILE cc_start: 0.7657 (mm) cc_final: 0.7184 (pt) REVERT: B 118 LYS cc_start: 0.6512 (ttpt) cc_final: 0.6250 (mtmm) REVERT: B 187 ARG cc_start: 0.6975 (mtt180) cc_final: 0.6758 (mtt90) REVERT: B 211 GLU cc_start: 0.6520 (mm-30) cc_final: 0.6305 (mt-10) REVERT: B 224 GLU cc_start: 0.6699 (pt0) cc_final: 0.6488 (mt-10) REVERT: B 228 LYS cc_start: 0.6537 (ttpt) cc_final: 0.5940 (ttpp) REVERT: B 295 ARG cc_start: 0.6773 (mtp-110) cc_final: 0.6117 (mtt180) REVERT: C 22 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7126 (mp10) REVERT: C 73 CYS cc_start: 0.6303 (m) cc_final: 0.5780 (p) REVERT: C 83 GLU cc_start: 0.7140 (tt0) cc_final: 0.6262 (tp30) REVERT: C 91 LYS cc_start: 0.7445 (ttpt) cc_final: 0.6542 (tptm) REVERT: C 250 SER cc_start: 0.8246 (p) cc_final: 0.7953 (m) REVERT: C 251 GLN cc_start: 0.7848 (mt0) cc_final: 0.6647 (pp30) REVERT: C 252 LEU cc_start: 0.6943 (mm) cc_final: 0.6424 (mt) REVERT: C 327 MET cc_start: 0.7641 (mtp) cc_final: 0.7399 (mtp) REVERT: C 359 ASN cc_start: 0.6661 (m110) cc_final: 0.6178 (t0) REVERT: D 3 SER cc_start: 0.8362 (t) cc_final: 0.8156 (p) REVERT: D 23 ASN cc_start: 0.7655 (t0) cc_final: 0.7400 (t0) REVERT: D 28 ASP cc_start: 0.8003 (t0) cc_final: 0.7706 (t70) REVERT: D 47 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7238 (mttp) REVERT: D 56 MET cc_start: 0.8321 (ttm) cc_final: 0.8012 (ttm) REVERT: D 73 GLN cc_start: 0.7361 (tt0) cc_final: 0.7051 (mt0) REVERT: D 113 MET cc_start: 0.7281 (tpp) cc_final: 0.6767 (mmt) REVERT: D 143 ASN cc_start: 0.7243 (t0) cc_final: 0.7011 (t0) REVERT: D 157 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6795 (mtm) REVERT: D 172 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6420 (mt-10) REVERT: D 255 ARG cc_start: 0.5740 (mtm110) cc_final: 0.5483 (mtt90) REVERT: D 283 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7230 (mmt180) REVERT: D 284 MET cc_start: 0.7757 (mtt) cc_final: 0.7529 (mtt) REVERT: E 88 ASN cc_start: 0.5608 (t0) cc_final: 0.5395 (t0) REVERT: E 94 ARG cc_start: 0.7601 (mtp180) cc_final: 0.6996 (mtp180) REVERT: E 98 SER cc_start: 0.7067 (t) cc_final: 0.6655 (m) REVERT: F 31 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.6628 (pm20) REVERT: F 57 GLU cc_start: 0.7241 (tp30) cc_final: 0.6876 (mp0) REVERT: F 58 GLN cc_start: 0.7552 (mp-120) cc_final: 0.6096 (tp-100) REVERT: F 81 GLU cc_start: 0.6930 (mp0) cc_final: 0.6126 (mm-30) REVERT: F 88 ARG cc_start: 0.7273 (ttt-90) cc_final: 0.6223 (ttm110) REVERT: F 97 ARG cc_start: 0.7328 (mmm160) cc_final: 0.6893 (mmm160) REVERT: F 107 LYS cc_start: 0.7154 (mmmm) cc_final: 0.6900 (mptm) REVERT: F 148 GLU cc_start: 0.6881 (tt0) cc_final: 0.6680 (tt0) REVERT: G 18 GLU cc_start: 0.7433 (pt0) cc_final: 0.6381 (mm-30) REVERT: G 20 ASP cc_start: 0.7673 (m-30) cc_final: 0.7259 (t0) REVERT: G 71 GLU cc_start: 0.6050 (mp0) cc_final: 0.5649 (pm20) REVERT: G 82 ASP cc_start: 0.6164 (m-30) cc_final: 0.5824 (m-30) REVERT: G 102 GLU cc_start: 0.7015 (tt0) cc_final: 0.6373 (mp0) REVERT: G 132 LYS cc_start: 0.7202 (mttm) cc_final: 0.6871 (mtmm) REVERT: G 135 GLU cc_start: 0.7082 (tt0) cc_final: 0.6706 (tt0) REVERT: H 72 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: H 83 GLU cc_start: 0.6827 (pt0) cc_final: 0.6583 (tm-30) REVERT: H 121 GLN cc_start: 0.6607 (tt0) cc_final: 0.6276 (tm-30) REVERT: H 141 SER cc_start: 0.7935 (t) cc_final: 0.7706 (m) REVERT: H 165 ILE cc_start: 0.7578 (tt) cc_final: 0.7359 (mt) REVERT: H 191 LYS cc_start: 0.6548 (tttp) cc_final: 0.6092 (ttmt) REVERT: H 206 ARG cc_start: 0.6742 (ttm-80) cc_final: 0.5637 (ttm110) REVERT: H 225 ASN cc_start: 0.7570 (m-40) cc_final: 0.6875 (t0) REVERT: H 234 SER cc_start: 0.6728 (m) cc_final: 0.6404 (t) REVERT: H 269 MET cc_start: 0.8362 (ttm) cc_final: 0.8103 (ttp) REVERT: H 313 MET cc_start: 0.7697 (tpt) cc_final: 0.7474 (tpt) REVERT: H 328 LYS cc_start: 0.6863 (mmmm) cc_final: 0.6546 (mppt) REVERT: I 11 ASP cc_start: 0.6266 (t0) cc_final: 0.6038 (t0) REVERT: I 25 ASP cc_start: 0.6784 (m-30) cc_final: 0.6560 (p0) REVERT: I 50 LYS cc_start: 0.7482 (mmpt) cc_final: 0.7021 (mtpm) REVERT: I 68 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7237 (mttt) REVERT: I 92 ASN cc_start: 0.7425 (m-40) cc_final: 0.7170 (m-40) REVERT: I 122 ILE cc_start: 0.7580 (pt) cc_final: 0.7204 (mm) REVERT: I 169 TYR cc_start: 0.6596 (m-80) cc_final: 0.5396 (t80) REVERT: I 215 LYS cc_start: 0.7700 (mtpp) cc_final: 0.7293 (mttp) REVERT: I 296 ASN cc_start: 0.7243 (t0) cc_final: 0.6879 (t0) REVERT: I 305 MET cc_start: 0.8155 (mmm) cc_final: 0.7826 (mmm) REVERT: I 336 LYS cc_start: 0.6832 (ptpp) cc_final: 0.6530 (ttpt) REVERT: I 362 TYR cc_start: 0.6950 (t80) cc_final: 0.6669 (t80) REVERT: M 78 ASN cc_start: 0.7435 (t0) cc_final: 0.6952 (t0) REVERT: M 96 VAL cc_start: 0.7487 (m) cc_final: 0.7275 (m) REVERT: M 194 THR cc_start: 0.8079 (m) cc_final: 0.7633 (p) REVERT: M 202 THR cc_start: 0.7555 (m) cc_final: 0.7220 (p) REVERT: M 224 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7414 (pm20) REVERT: M 263 GLN cc_start: 0.7739 (mt0) cc_final: 0.7315 (mt0) REVERT: N 47 MET cc_start: 0.1361 (ttp) cc_final: 0.0488 (ttm) REVERT: N 225 ASN cc_start: 0.6778 (t0) cc_final: 0.6478 (m-40) REVERT: N 276 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6980 (mt-10) REVERT: N 328 LYS cc_start: 0.7428 (tptt) cc_final: 0.6951 (tppp) REVERT: N 355 MET cc_start: 0.8059 (mtt) cc_final: 0.7802 (mtp) REVERT: N 360 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7123 (tp-100) REVERT: O 41 GLN cc_start: 0.6989 (tp40) cc_final: 0.6730 (mm-40) REVERT: O 68 LYS cc_start: 0.7976 (ptmt) cc_final: 0.7691 (ptpp) REVERT: O 100 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7609 (mt-10) REVERT: O 113 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7240 (mmtp) REVERT: O 118 LYS cc_start: 0.7282 (mttm) cc_final: 0.6682 (mtpm) REVERT: O 206 ARG cc_start: 0.7598 (ttp-170) cc_final: 0.6586 (ttp-110) REVERT: O 276 GLU cc_start: 0.6904 (tt0) cc_final: 0.6431 (tt0) REVERT: O 284 LYS cc_start: 0.7966 (mttm) cc_final: 0.7534 (mtpm) REVERT: O 286 ASP cc_start: 0.6881 (t0) cc_final: 0.6518 (m-30) REVERT: O 326 LYS cc_start: 0.7368 (ptpp) cc_final: 0.6438 (mmmt) REVERT: O 328 LYS cc_start: 0.7709 (mtmt) cc_final: 0.7084 (mttp) REVERT: O 359 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7672 (tptp) REVERT: P 82 MET cc_start: 0.7772 (tpt) cc_final: 0.6931 (tpt) REVERT: P 283 MET cc_start: 0.8200 (mmm) cc_final: 0.7974 (mmp) REVERT: P 326 LYS cc_start: 0.7660 (pttp) cc_final: 0.7454 (pttm) REVERT: P 359 LYS cc_start: 0.7195 (ptmm) cc_final: 0.6816 (tttt) REVERT: Q 6 THR cc_start: 0.8029 (p) cc_final: 0.7559 (t) REVERT: Q 34 ILE cc_start: 0.8353 (mt) cc_final: 0.7899 (pt) REVERT: Q 47 MET cc_start: 0.6248 (mmm) cc_final: 0.5405 (ptt) REVERT: Q 60 SER cc_start: 0.7986 (t) cc_final: 0.7690 (p) REVERT: Q 66 THR cc_start: 0.8303 (t) cc_final: 0.8056 (m) REVERT: Q 82 MET cc_start: 0.8272 (tpt) cc_final: 0.7748 (tpt) REVERT: Q 95 ARG cc_start: 0.6926 (ptp-170) cc_final: 0.6378 (ptp-110) REVERT: Q 167 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7331 (mm-30) REVERT: Q 190 MET cc_start: 0.7630 (mtm) cc_final: 0.7387 (mtp) REVERT: Q 215 LYS cc_start: 0.7162 (mmmt) cc_final: 0.6949 (mmtp) REVERT: Q 224 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7795 (mp0) REVERT: Q 246 GLN cc_start: 0.7922 (mt0) cc_final: 0.7618 (mt0) REVERT: Q 291 LYS cc_start: 0.5649 (mttm) cc_final: 0.4643 (tmtm) REVERT: Q 314 GLN cc_start: 0.7972 (tt0) cc_final: 0.7624 (tt0) REVERT: Q 328 LYS cc_start: 0.7334 (ttmt) cc_final: 0.6601 (ttpp) REVERT: Q 336 LYS cc_start: 0.7676 (tptm) cc_final: 0.7349 (tppp) REVERT: Q 354 GLN cc_start: 0.7645 (pm20) cc_final: 0.7059 (mm110) REVERT: R 25 ASP cc_start: 0.7944 (m-30) cc_final: 0.7599 (t70) REVERT: R 83 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7002 (mt-10) REVERT: R 100 GLU cc_start: 0.8143 (pt0) cc_final: 0.7825 (pt0) REVERT: R 167 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7248 (mm-30) REVERT: R 206 ARG cc_start: 0.6814 (tpp80) cc_final: 0.6356 (ttp-170) REVERT: R 215 LYS cc_start: 0.7612 (mmmt) cc_final: 0.7301 (mptm) REVERT: R 234 SER cc_start: 0.5746 (OUTLIER) cc_final: 0.5418 (t) outliers start: 113 outliers final: 36 residues processed: 1162 average time/residue: 2.7260 time to fit residues: 3884.5037 Evaluate side-chains 725 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 681 time to evaluate : 4.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 283 ARG Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 234 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 412 optimal weight: 1.9990 chunk 370 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 198 optimal weight: 0.9990 chunk 383 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 444 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 313 ASN B 10 ASN B 48 GLN B 83 ASN B 173 HIS B 201 ASN B 335 ASN B 364 ASN C 209 HIS C 334 GLN D 106 GLN D 292 GLN F 10 ASN F 60 GLN F 120 ASN G 19 GLN G 106 ASN H 137 GLN I 41 GLN M 59 GLN N 137 GLN O 353 GLN O 360 GLN P 263 GLN Q 41 GLN Q 87 HIS Q 173 HIS R 49 GLN R 354 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 39895 Z= 0.245 Angle : 0.690 7.590 54139 Z= 0.358 Chirality : 0.045 0.164 5990 Planarity : 0.006 0.060 6962 Dihedral : 10.899 158.714 5608 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.10 % Allowed : 13.53 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.12), residues: 4854 helix: -0.80 (0.11), residues: 1972 sheet: -0.50 (0.17), residues: 870 loop : 0.53 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 356 HIS 0.006 0.001 HIS N 161 PHE 0.023 0.001 PHE B 277 TYR 0.019 0.001 TYR E 133 ARG 0.009 0.001 ARG F 156 *********************** 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 845 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 715 time to evaluate : 4.773 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: A 100 GLU cc_start: 0.7248 (pt0) cc_final: 0.6997 (pp20) REVERT: A 226 ASP cc_start: 0.6887 (m-30) cc_final: 0.6499 (m-30) REVERT: A 238 GLU cc_start: 0.5827 (OUTLIER) cc_final: 0.4904 (tt0) REVERT: A 239 ARG cc_start: 0.6043 (mtt180) cc_final: 0.5550 (mtm-85) REVERT: A 242 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.5432 (mp0) REVERT: A 253 LYS cc_start: 0.6533 (mppt) cc_final: 0.6084 (mptt) REVERT: A 297 GLU cc_start: 0.6738 (mt-10) cc_final: 0.5774 (mp0) REVERT: A 302 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.6268 (m-30) REVERT: A 340 LYS cc_start: 0.7317 (tptp) cc_final: 0.6769 (ttpt) REVERT: A 356 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6940 (tm-30) REVERT: A 406 LYS cc_start: 0.6796 (pttp) cc_final: 0.6402 (ptpt) REVERT: B 6 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7191 (mt) REVERT: B 68 LYS cc_start: 0.6563 (mtmt) cc_final: 0.6163 (mtmt) REVERT: B 73 ASN cc_start: 0.7232 (m-40) cc_final: 0.6784 (t0) REVERT: B 96 ILE cc_start: 0.7596 (mm) cc_final: 0.7079 (pt) REVERT: B 118 LYS cc_start: 0.6192 (ttpt) cc_final: 0.5923 (mtmt) REVERT: B 152 VAL cc_start: 0.8034 (OUTLIER) cc_final: 0.7775 (p) REVERT: B 228 LYS cc_start: 0.6504 (ttpt) cc_final: 0.5797 (ttpp) REVERT: B 295 ARG cc_start: 0.6633 (mtp180) cc_final: 0.5663 (mpt-90) REVERT: B 364 ASN cc_start: 0.7156 (m-40) cc_final: 0.6563 (t0) REVERT: C 22 GLN cc_start: 0.7429 (mm-40) cc_final: 0.7148 (mp10) REVERT: C 83 GLU cc_start: 0.7036 (tt0) cc_final: 0.6122 (mp0) REVERT: C 91 LYS cc_start: 0.7333 (ttpt) cc_final: 0.5955 (tptm) REVERT: C 250 SER cc_start: 0.8164 (p) cc_final: 0.7922 (m) REVERT: C 251 GLN cc_start: 0.7547 (mt0) cc_final: 0.6821 (mp10) REVERT: C 327 MET cc_start: 0.7455 (mtp) cc_final: 0.7180 (mtp) REVERT: C 359 ASN cc_start: 0.6574 (m110) cc_final: 0.5833 (t0) REVERT: D 13 GLU cc_start: 0.6627 (mm-30) cc_final: 0.6183 (mt-10) REVERT: D 28 ASP cc_start: 0.8242 (t0) cc_final: 0.8033 (t70) REVERT: D 47 LYS cc_start: 0.7879 (mtmm) cc_final: 0.7255 (mttp) REVERT: D 73 GLN cc_start: 0.7272 (tt0) cc_final: 0.7029 (mt0) REVERT: D 84 MET cc_start: 0.7279 (mpp) cc_final: 0.6950 (tmm) REVERT: D 113 MET cc_start: 0.7042 (tpp) cc_final: 0.6626 (mmt) REVERT: D 172 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6327 (mt-10) REVERT: D 185 ARG cc_start: 0.7750 (ptp-170) cc_final: 0.7386 (ptp-170) REVERT: D 255 ARG cc_start: 0.5576 (mtm110) cc_final: 0.5223 (mtt90) REVERT: E 61 GLU cc_start: 0.7127 (tt0) cc_final: 0.6502 (pt0) REVERT: E 94 ARG cc_start: 0.7491 (mtp180) cc_final: 0.7015 (mtp180) REVERT: E 98 SER cc_start: 0.6775 (t) cc_final: 0.6477 (m) REVERT: F 17 THR cc_start: 0.7230 (OUTLIER) cc_final: 0.7023 (t) REVERT: F 58 GLN cc_start: 0.7391 (mp-120) cc_final: 0.5919 (tp-100) REVERT: F 81 GLU cc_start: 0.6595 (mp0) cc_final: 0.5778 (mm-30) REVERT: F 83 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6805 (mt-10) REVERT: F 97 ARG cc_start: 0.7222 (mmm160) cc_final: 0.6743 (mmm160) REVERT: F 107 LYS cc_start: 0.6997 (mmmm) cc_final: 0.6716 (mttt) REVERT: F 148 GLU cc_start: 0.6808 (tt0) cc_final: 0.6523 (tt0) REVERT: G 54 GLN cc_start: 0.6487 (mm-40) cc_final: 0.5694 (tm-30) REVERT: G 102 GLU cc_start: 0.6779 (tt0) cc_final: 0.6082 (mp0) REVERT: G 135 GLU cc_start: 0.6584 (tt0) cc_final: 0.6315 (tt0) REVERT: H 45 VAL cc_start: 0.7657 (m) cc_final: 0.7413 (t) REVERT: H 72 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: H 123 MET cc_start: 0.7886 (tpp) cc_final: 0.6980 (mmt) REVERT: H 141 SER cc_start: 0.7674 (t) cc_final: 0.7325 (m) REVERT: H 206 ARG cc_start: 0.6569 (ttm-80) cc_final: 0.5510 (ttm110) REVERT: H 225 ASN cc_start: 0.7414 (m-40) cc_final: 0.6863 (t0) REVERT: H 234 SER cc_start: 0.6810 (m) cc_final: 0.6506 (t) REVERT: H 269 MET cc_start: 0.8307 (ttm) cc_final: 0.8099 (ttm) REVERT: H 305 MET cc_start: 0.8625 (tpt) cc_final: 0.8344 (mmm) REVERT: H 328 LYS cc_start: 0.6828 (mmmm) cc_final: 0.6596 (mppt) REVERT: I 11 ASP cc_start: 0.6422 (t0) cc_final: 0.6219 (t0) REVERT: I 25 ASP cc_start: 0.6898 (m-30) cc_final: 0.6591 (p0) REVERT: I 50 LYS cc_start: 0.7333 (mmpt) cc_final: 0.6937 (mtpm) REVERT: I 68 LYS cc_start: 0.7889 (mmmt) cc_final: 0.7305 (mttt) REVERT: I 95 ARG cc_start: 0.6402 (mtp85) cc_final: 0.6112 (mtt-85) REVERT: I 132 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.5432 (pmm) REVERT: I 169 TYR cc_start: 0.6504 (m-80) cc_final: 0.5287 (t80) REVERT: I 215 LYS cc_start: 0.7632 (mtpp) cc_final: 0.7237 (mttp) REVERT: I 305 MET cc_start: 0.8228 (mmm) cc_final: 0.7985 (mmm) REVERT: I 336 LYS cc_start: 0.6871 (ptpp) cc_final: 0.6622 (ttpt) REVERT: M 78 ASN cc_start: 0.7559 (t0) cc_final: 0.7143 (t0) REVERT: M 83 GLU cc_start: 0.6833 (tt0) cc_final: 0.6395 (tm-30) REVERT: M 194 THR cc_start: 0.8020 (m) cc_final: 0.7526 (p) REVERT: M 202 THR cc_start: 0.6848 (m) cc_final: 0.6453 (p) REVERT: M 206 ARG cc_start: 0.7675 (ttm110) cc_final: 0.7202 (ttm110) REVERT: M 224 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7219 (pm20) REVERT: M 227 MET cc_start: 0.8374 (mmt) cc_final: 0.7814 (mmt) REVERT: N 41 GLN cc_start: 0.7046 (pt0) cc_final: 0.6800 (pm20) REVERT: N 47 MET cc_start: 0.1192 (ttp) cc_final: 0.0513 (ttm) REVERT: N 225 ASN cc_start: 0.6987 (t0) cc_final: 0.6539 (m-40) REVERT: N 276 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6975 (mt-10) REVERT: N 299 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8299 (mtt) REVERT: N 328 LYS cc_start: 0.7467 (tptt) cc_final: 0.7029 (tptm) REVERT: N 360 GLN cc_start: 0.7450 (tm-30) cc_final: 0.7156 (tp-100) REVERT: O 41 GLN cc_start: 0.6843 (tp40) cc_final: 0.6577 (mm-40) REVERT: O 68 LYS cc_start: 0.7987 (ptmt) cc_final: 0.7704 (ptpp) REVERT: O 100 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7589 (mt-10) REVERT: O 113 LYS cc_start: 0.7532 (mmtt) cc_final: 0.7126 (mmtp) REVERT: O 118 LYS cc_start: 0.7119 (mttm) cc_final: 0.6629 (mtpm) REVERT: O 206 ARG cc_start: 0.7320 (ttp-170) cc_final: 0.6362 (ttp-110) REVERT: O 276 GLU cc_start: 0.6969 (tt0) cc_final: 0.6481 (tt0) REVERT: O 284 LYS cc_start: 0.7975 (mttm) cc_final: 0.7560 (mtpm) REVERT: O 286 ASP cc_start: 0.6740 (t0) cc_final: 0.6424 (m-30) REVERT: O 326 LYS cc_start: 0.7209 (ptpp) cc_final: 0.6333 (mmmt) REVERT: O 328 LYS cc_start: 0.7610 (mtmt) cc_final: 0.6870 (tptm) REVERT: O 359 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7566 (tptp) REVERT: P 82 MET cc_start: 0.7759 (tpt) cc_final: 0.7069 (tpt) REVERT: P 221 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7975 (tp) REVERT: P 224 GLU cc_start: 0.6991 (tp30) cc_final: 0.6736 (mm-30) REVERT: P 355 MET cc_start: 0.8163 (mtm) cc_final: 0.7801 (mtt) REVERT: P 359 LYS cc_start: 0.7254 (ptmm) cc_final: 0.6811 (tptt) REVERT: Q 6 THR cc_start: 0.7922 (p) cc_final: 0.7442 (t) REVERT: Q 34 ILE cc_start: 0.8360 (mt) cc_final: 0.7944 (pt) REVERT: Q 47 MET cc_start: 0.6246 (mmm) cc_final: 0.5399 (ptt) REVERT: Q 60 SER cc_start: 0.7785 (t) cc_final: 0.7548 (p) REVERT: Q 82 MET cc_start: 0.8285 (tpt) cc_final: 0.7874 (tpt) REVERT: Q 167 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7170 (mm-30) REVERT: Q 190 MET cc_start: 0.7335 (mtm) cc_final: 0.6958 (mtp) REVERT: Q 246 GLN cc_start: 0.7880 (mt0) cc_final: 0.7513 (mt0) REVERT: Q 286 ASP cc_start: 0.7112 (t0) cc_final: 0.6735 (m-30) REVERT: Q 291 LYS cc_start: 0.5401 (mttm) cc_final: 0.4628 (tmtm) REVERT: Q 313 MET cc_start: 0.7920 (tpt) cc_final: 0.7527 (mmm) REVERT: Q 328 LYS cc_start: 0.7254 (ttmt) cc_final: 0.6540 (ttpp) REVERT: Q 336 LYS cc_start: 0.7601 (tptm) cc_final: 0.7247 (tppt) REVERT: Q 354 GLN cc_start: 0.7631 (pm20) cc_final: 0.7203 (mm110) REVERT: R 16 LEU cc_start: 0.7867 (tp) cc_final: 0.7505 (mt) REVERT: R 99 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: R 206 ARG cc_start: 0.6615 (tpp80) cc_final: 0.6091 (ttp-170) REVERT: R 215 LYS cc_start: 0.7635 (mmmt) cc_final: 0.7395 (mptm) REVERT: R 225 ASN cc_start: 0.6314 (t0) cc_final: 0.5992 (m-40) outliers start: 130 outliers final: 48 residues processed: 791 average time/residue: 2.7383 time to fit residues: 2652.7921 Evaluate side-chains 680 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 620 time to evaluate : 4.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 51 ASP Chi-restraints excluded: chain P residue 221 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 199 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 246 optimal weight: 9.9990 chunk 137 optimal weight: 0.7980 chunk 369 optimal weight: 1.9990 chunk 302 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 444 optimal weight: 3.9990 chunk 480 optimal weight: 2.9990 chunk 396 optimal weight: 1.9990 chunk 441 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 356 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 172 ASN D 254 ASN E 139 GLN F 120 ASN G 31 GLN I 41 GLN I 161 HIS M 88 HIS M 173 HIS M 297 ASN O 225 ASN P 173 HIS R 354 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 39895 Z= 0.277 Angle : 0.631 7.267 54139 Z= 0.320 Chirality : 0.046 0.177 5990 Planarity : 0.005 0.051 6962 Dihedral : 9.852 165.725 5572 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.05 % Allowed : 14.32 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.12), residues: 4854 helix: -0.33 (0.11), residues: 1969 sheet: -0.54 (0.17), residues: 890 loop : 0.64 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 340 HIS 0.007 0.001 HIS O 161 PHE 0.019 0.001 PHE F 101 TYR 0.027 0.001 TYR B 377 ARG 0.006 0.000 ARG G 4 *********************** 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 765 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 637 time to evaluate : 4.812 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 100 GLU cc_start: 0.7337 (pt0) cc_final: 0.7081 (pp20) REVERT: A 137 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.5862 (mp0) REVERT: A 207 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6612 (tppt) REVERT: A 226 ASP cc_start: 0.6937 (m-30) cc_final: 0.6631 (m-30) REVERT: A 239 ARG cc_start: 0.5948 (mtt180) cc_final: 0.5465 (mtm-85) REVERT: A 253 LYS cc_start: 0.6553 (OUTLIER) cc_final: 0.6120 (mptt) REVERT: A 257 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6540 (ttt180) REVERT: A 302 ASP cc_start: 0.6736 (OUTLIER) cc_final: 0.6331 (m-30) REVERT: A 340 LYS cc_start: 0.7162 (tptp) cc_final: 0.6681 (ttpt) REVERT: A 406 LYS cc_start: 0.6914 (pttp) cc_final: 0.6465 (ptpt) REVERT: B 68 LYS cc_start: 0.6642 (mtmt) cc_final: 0.6156 (mtmt) REVERT: B 73 ASN cc_start: 0.7432 (m-40) cc_final: 0.6943 (t0) REVERT: B 96 ILE cc_start: 0.7634 (mm) cc_final: 0.7279 (pt) REVERT: B 118 LYS cc_start: 0.6265 (ttpt) cc_final: 0.6056 (mtmt) REVERT: B 147 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7644 (mt) REVERT: B 152 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7844 (p) REVERT: B 167 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: B 228 LYS cc_start: 0.6545 (ttpt) cc_final: 0.5849 (ttpp) REVERT: B 295 ARG cc_start: 0.6640 (mtp180) cc_final: 0.5658 (mpt-90) REVERT: B 364 ASN cc_start: 0.7356 (m-40) cc_final: 0.6735 (t0) REVERT: B 376 GLU cc_start: 0.7593 (pt0) cc_final: 0.7108 (pp20) REVERT: C 22 GLN cc_start: 0.7586 (mm-40) cc_final: 0.7269 (mp10) REVERT: C 83 GLU cc_start: 0.7023 (tt0) cc_final: 0.6186 (mp0) REVERT: C 91 LYS cc_start: 0.7393 (ttpt) cc_final: 0.5960 (tptp) REVERT: C 134 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7416 (t70) REVERT: C 251 GLN cc_start: 0.7419 (mt0) cc_final: 0.6939 (mp10) REVERT: C 276 LEU cc_start: 0.7058 (tp) cc_final: 0.6787 (tm) REVERT: C 327 MET cc_start: 0.7466 (mtp) cc_final: 0.7237 (mtm) REVERT: C 359 ASN cc_start: 0.6731 (m110) cc_final: 0.6060 (t0) REVERT: D 13 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6192 (mt-10) REVERT: D 47 LYS cc_start: 0.7864 (mtmm) cc_final: 0.7306 (mttp) REVERT: D 73 GLN cc_start: 0.7259 (tt0) cc_final: 0.6996 (mt0) REVERT: D 84 MET cc_start: 0.7254 (mpp) cc_final: 0.6982 (tmm) REVERT: D 113 MET cc_start: 0.6935 (tpp) cc_final: 0.6505 (mmt) REVERT: D 172 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6288 (mt-10) REVERT: D 185 ARG cc_start: 0.7696 (ptp-170) cc_final: 0.7373 (ptp-170) REVERT: D 255 ARG cc_start: 0.5624 (mtm110) cc_final: 0.5193 (mtt90) REVERT: D 269 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6508 (mp) REVERT: E 45 ASP cc_start: 0.6569 (t0) cc_final: 0.6093 (m-30) REVERT: E 61 GLU cc_start: 0.7112 (tt0) cc_final: 0.6289 (pt0) REVERT: E 94 ARG cc_start: 0.7574 (mtp180) cc_final: 0.7070 (mtp180) REVERT: E 98 SER cc_start: 0.6917 (t) cc_final: 0.6542 (m) REVERT: F 31 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8106 (pp20) REVERT: F 58 GLN cc_start: 0.7451 (mp-120) cc_final: 0.5979 (tp-100) REVERT: F 74 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7182 (mp) REVERT: F 81 GLU cc_start: 0.6718 (mp0) cc_final: 0.5836 (mm-30) REVERT: F 83 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6963 (mt-10) REVERT: F 97 ARG cc_start: 0.7310 (mmm160) cc_final: 0.6941 (mmm160) REVERT: F 107 LYS cc_start: 0.7114 (mmmm) cc_final: 0.6791 (mttt) REVERT: F 148 GLU cc_start: 0.6912 (tt0) cc_final: 0.6618 (tt0) REVERT: G 98 GLU cc_start: 0.6904 (pp20) cc_final: 0.6676 (pp20) REVERT: G 102 GLU cc_start: 0.6941 (tt0) cc_final: 0.6178 (mp0) REVERT: G 135 GLU cc_start: 0.6700 (tt0) cc_final: 0.6423 (tt0) REVERT: H 25 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: H 28 ARG cc_start: 0.7700 (tpp-160) cc_final: 0.7484 (tpp80) REVERT: H 45 VAL cc_start: 0.7701 (m) cc_final: 0.7478 (t) REVERT: H 72 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6545 (mp0) REVERT: H 141 SER cc_start: 0.7739 (t) cc_final: 0.7383 (m) REVERT: H 187 ASP cc_start: 0.7583 (m-30) cc_final: 0.7113 (m-30) REVERT: H 206 ARG cc_start: 0.6574 (ttm-80) cc_final: 0.5626 (ttm110) REVERT: H 225 ASN cc_start: 0.7502 (m-40) cc_final: 0.6900 (t0) REVERT: H 234 SER cc_start: 0.7088 (m) cc_final: 0.6771 (t) REVERT: H 269 MET cc_start: 0.8325 (ttm) cc_final: 0.8101 (ttp) REVERT: H 328 LYS cc_start: 0.6813 (mmmm) cc_final: 0.6593 (mppt) REVERT: I 25 ASP cc_start: 0.6882 (m-30) cc_final: 0.6582 (p0) REVERT: I 50 LYS cc_start: 0.7336 (mmpt) cc_final: 0.6972 (mtpt) REVERT: I 68 LYS cc_start: 0.7985 (mmmt) cc_final: 0.7392 (mttt) REVERT: I 132 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.5328 (pmm) REVERT: I 169 TYR cc_start: 0.6493 (m-80) cc_final: 0.5281 (t80) REVERT: I 180 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7024 (tt) REVERT: I 215 LYS cc_start: 0.7635 (mtpp) cc_final: 0.7308 (mttp) REVERT: I 305 MET cc_start: 0.8255 (mmm) cc_final: 0.7926 (mmm) REVERT: I 336 LYS cc_start: 0.6811 (ptpp) cc_final: 0.6482 (ttpt) REVERT: M 78 ASN cc_start: 0.7610 (t0) cc_final: 0.7221 (t0) REVERT: M 83 GLU cc_start: 0.6955 (tt0) cc_final: 0.6413 (tm-30) REVERT: M 194 THR cc_start: 0.8094 (m) cc_final: 0.7620 (p) REVERT: M 202 THR cc_start: 0.7197 (m) cc_final: 0.6755 (p) REVERT: M 206 ARG cc_start: 0.7692 (ttm110) cc_final: 0.7131 (ttm110) REVERT: M 227 MET cc_start: 0.8395 (mmt) cc_final: 0.7875 (mmt) REVERT: N 41 GLN cc_start: 0.7063 (pt0) cc_final: 0.6855 (pm20) REVERT: N 47 MET cc_start: 0.1201 (ttp) cc_final: 0.0501 (ttm) REVERT: N 211 ASP cc_start: 0.7568 (m-30) cc_final: 0.7311 (t70) REVERT: N 225 ASN cc_start: 0.7146 (t0) cc_final: 0.6790 (m-40) REVERT: N 276 GLU cc_start: 0.7231 (mt-10) cc_final: 0.7023 (mt-10) REVERT: N 299 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8359 (mtt) REVERT: N 328 LYS cc_start: 0.7446 (tptt) cc_final: 0.7031 (tptm) REVERT: N 360 GLN cc_start: 0.7527 (tm-30) cc_final: 0.7254 (tp-100) REVERT: O 68 LYS cc_start: 0.7947 (ptmt) cc_final: 0.7669 (ptpp) REVERT: O 100 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7660 (mt-10) REVERT: O 113 LYS cc_start: 0.7432 (mmtt) cc_final: 0.7126 (mmtp) REVERT: O 206 ARG cc_start: 0.7460 (ttp-170) cc_final: 0.6315 (ttp-110) REVERT: O 276 GLU cc_start: 0.7013 (tt0) cc_final: 0.6686 (tt0) REVERT: O 284 LYS cc_start: 0.8081 (mttm) cc_final: 0.7765 (mtpm) REVERT: O 286 ASP cc_start: 0.6767 (t0) cc_final: 0.6454 (m-30) REVERT: O 326 LYS cc_start: 0.7392 (ptpp) cc_final: 0.6519 (mmmt) REVERT: O 328 LYS cc_start: 0.7721 (mtmt) cc_final: 0.6895 (tptm) REVERT: O 359 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7628 (tptp) REVERT: P 82 MET cc_start: 0.7875 (tpt) cc_final: 0.7227 (tpt) REVERT: P 224 GLU cc_start: 0.7017 (tp30) cc_final: 0.6777 (mm-30) REVERT: P 241 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: P 355 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7837 (mtt) REVERT: P 359 LYS cc_start: 0.7277 (ptmm) cc_final: 0.6843 (tptt) REVERT: Q 6 THR cc_start: 0.8058 (p) cc_final: 0.7548 (t) REVERT: Q 34 ILE cc_start: 0.8414 (mt) cc_final: 0.8111 (pt) REVERT: Q 47 MET cc_start: 0.6413 (mmm) cc_final: 0.5376 (ptt) REVERT: Q 60 SER cc_start: 0.7803 (t) cc_final: 0.7584 (p) REVERT: Q 72 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6879 (mt-10) REVERT: Q 190 MET cc_start: 0.7374 (mtm) cc_final: 0.7022 (mtp) REVERT: Q 225 ASN cc_start: 0.7074 (t0) cc_final: 0.6871 (t0) REVERT: Q 286 ASP cc_start: 0.7364 (t0) cc_final: 0.6918 (m-30) REVERT: Q 291 LYS cc_start: 0.5394 (mttm) cc_final: 0.4655 (tmtm) REVERT: Q 313 MET cc_start: 0.7968 (tpt) cc_final: 0.7677 (mmm) REVERT: Q 328 LYS cc_start: 0.7276 (ttmt) cc_final: 0.6503 (ttpp) REVERT: Q 336 LYS cc_start: 0.7686 (tptm) cc_final: 0.7343 (tppt) REVERT: Q 354 GLN cc_start: 0.7606 (pm20) cc_final: 0.7246 (mm110) REVERT: Q 368 SER cc_start: 0.7728 (OUTLIER) cc_final: 0.7517 (t) REVERT: R 37 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.5941 (mpp-170) REVERT: R 47 MET cc_start: 0.4363 (mmt) cc_final: 0.4157 (ppp) REVERT: R 72 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7397 (mt-10) REVERT: R 99 GLU cc_start: 0.7330 (pt0) cc_final: 0.7030 (pm20) REVERT: R 107 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.6289 (tp30) REVERT: R 206 ARG cc_start: 0.6740 (tpp80) cc_final: 0.6206 (ttm-80) REVERT: R 215 LYS cc_start: 0.7564 (mmmt) cc_final: 0.7320 (mptm) REVERT: R 225 ASN cc_start: 0.6496 (t0) cc_final: 0.6124 (m-40) REVERT: R 288 ASP cc_start: 0.7775 (p0) cc_final: 0.7468 (m-30) outliers start: 128 outliers final: 53 residues processed: 718 average time/residue: 2.7855 time to fit residues: 2435.9506 Evaluate side-chains 657 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 580 time to evaluate : 4.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 241 GLU Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 147 ARG Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 199 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 439 optimal weight: 2.9990 chunk 334 optimal weight: 2.9990 chunk 230 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 chunk 446 optimal weight: 2.9990 chunk 472 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 423 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 143 ASN D 254 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 297 ASN I 41 GLN ** I 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 296 ASN Q 41 GLN R 275 HIS R 354 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 39895 Z= 0.333 Angle : 0.632 7.794 54139 Z= 0.318 Chirality : 0.046 0.189 5990 Planarity : 0.005 0.085 6962 Dihedral : 9.529 166.385 5565 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.26 % Allowed : 14.55 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.12), residues: 4854 helix: -0.17 (0.12), residues: 1968 sheet: -0.38 (0.16), residues: 929 loop : 0.59 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 340 HIS 0.008 0.001 HIS O 161 PHE 0.018 0.002 PHE F 101 TYR 0.016 0.001 TYR F 8 ARG 0.007 0.001 ARG C 192 *********************** 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 734 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 597 time to evaluate : 4.740 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: A 100 GLU cc_start: 0.7350 (pt0) cc_final: 0.7083 (pp20) REVERT: A 137 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5844 (mp0) REVERT: A 207 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6668 (tppt) REVERT: A 239 ARG cc_start: 0.5918 (mtt180) cc_final: 0.5418 (mtm-85) REVERT: A 242 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.5929 (mp0) REVERT: A 253 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6143 (mptt) REVERT: A 302 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.6460 (m-30) REVERT: A 340 LYS cc_start: 0.7176 (tptp) cc_final: 0.6672 (ttpt) REVERT: A 406 LYS cc_start: 0.6908 (pttp) cc_final: 0.6665 (ptpp) REVERT: B 68 LYS cc_start: 0.6641 (mtmt) cc_final: 0.6177 (mtmt) REVERT: B 73 ASN cc_start: 0.7534 (m-40) cc_final: 0.7039 (t0) REVERT: B 75 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.6706 (pt) REVERT: B 96 ILE cc_start: 0.7782 (mm) cc_final: 0.7269 (pt) REVERT: B 228 LYS cc_start: 0.6631 (ttpt) cc_final: 0.5911 (ttpp) REVERT: B 295 ARG cc_start: 0.6645 (mtp180) cc_final: 0.5606 (mpt-90) REVERT: B 364 ASN cc_start: 0.7373 (m-40) cc_final: 0.6750 (t0) REVERT: B 376 GLU cc_start: 0.7408 (pt0) cc_final: 0.6881 (pp20) REVERT: C 22 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7294 (mp10) REVERT: C 83 GLU cc_start: 0.7015 (tt0) cc_final: 0.6202 (mp0) REVERT: C 91 LYS cc_start: 0.7415 (ttpt) cc_final: 0.6111 (tttt) REVERT: C 251 GLN cc_start: 0.7412 (mt0) cc_final: 0.6928 (mp10) REVERT: C 359 ASN cc_start: 0.6767 (m110) cc_final: 0.6021 (t0) REVERT: D 13 GLU cc_start: 0.6627 (mm-30) cc_final: 0.6190 (mt-10) REVERT: D 47 LYS cc_start: 0.7841 (mtmm) cc_final: 0.7309 (mttp) REVERT: D 73 GLN cc_start: 0.7225 (tt0) cc_final: 0.6987 (mt0) REVERT: D 84 MET cc_start: 0.7257 (mpp) cc_final: 0.6995 (tmm) REVERT: D 113 MET cc_start: 0.6880 (tpp) cc_final: 0.6547 (mmt) REVERT: D 172 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6411 (mt-10) REVERT: D 255 ARG cc_start: 0.5697 (mtm110) cc_final: 0.5211 (mtt90) REVERT: D 269 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6527 (mp) REVERT: E 58 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7339 (ptm160) REVERT: E 94 ARG cc_start: 0.7594 (mtp180) cc_final: 0.7069 (mtp180) REVERT: E 98 SER cc_start: 0.6961 (t) cc_final: 0.6561 (m) REVERT: F 58 GLN cc_start: 0.7471 (mp-120) cc_final: 0.6199 (tp-100) REVERT: F 81 GLU cc_start: 0.6775 (mp0) cc_final: 0.5897 (mm-30) REVERT: F 97 ARG cc_start: 0.7365 (mmm160) cc_final: 0.6963 (mmm160) REVERT: F 107 LYS cc_start: 0.7108 (mmmm) cc_final: 0.6768 (mttt) REVERT: F 119 THR cc_start: 0.7384 (m) cc_final: 0.7054 (p) REVERT: F 148 GLU cc_start: 0.6879 (tt0) cc_final: 0.6615 (tt0) REVERT: G 54 GLN cc_start: 0.6514 (mm-40) cc_final: 0.5717 (tm-30) REVERT: G 102 GLU cc_start: 0.6974 (tt0) cc_final: 0.6226 (mp0) REVERT: G 135 GLU cc_start: 0.6694 (tt0) cc_final: 0.6421 (tt0) REVERT: H 28 ARG cc_start: 0.7636 (tpp-160) cc_final: 0.7276 (tpp80) REVERT: H 45 VAL cc_start: 0.7726 (m) cc_final: 0.7515 (t) REVERT: H 68 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7502 (mttm) REVERT: H 72 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: H 141 SER cc_start: 0.7787 (t) cc_final: 0.7415 (m) REVERT: H 206 ARG cc_start: 0.6601 (ttm-80) cc_final: 0.6084 (ttp-170) REVERT: H 225 ASN cc_start: 0.7570 (m-40) cc_final: 0.6910 (t0) REVERT: H 234 SER cc_start: 0.7180 (m) cc_final: 0.6854 (t) REVERT: H 306 TYR cc_start: 0.8850 (m-80) cc_final: 0.8532 (m-80) REVERT: H 328 LYS cc_start: 0.6835 (mmmm) cc_final: 0.6631 (mppt) REVERT: I 25 ASP cc_start: 0.6894 (m-30) cc_final: 0.6585 (p0) REVERT: I 50 LYS cc_start: 0.7324 (mmpt) cc_final: 0.6942 (mtpt) REVERT: I 68 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7461 (mttt) REVERT: I 215 LYS cc_start: 0.7684 (mtpp) cc_final: 0.7320 (mttp) REVERT: I 305 MET cc_start: 0.8307 (mmm) cc_final: 0.7937 (mmm) REVERT: I 336 LYS cc_start: 0.6838 (ptpp) cc_final: 0.6531 (ttpt) REVERT: M 78 ASN cc_start: 0.7643 (t0) cc_final: 0.7237 (t0) REVERT: M 80 ASP cc_start: 0.6822 (OUTLIER) cc_final: 0.6586 (t70) REVERT: M 194 THR cc_start: 0.8140 (m) cc_final: 0.7712 (p) REVERT: M 202 THR cc_start: 0.7288 (m) cc_final: 0.6816 (p) REVERT: M 206 ARG cc_start: 0.7671 (ttm110) cc_final: 0.7052 (ttm110) REVERT: M 227 MET cc_start: 0.8407 (mmt) cc_final: 0.8114 (mmt) REVERT: N 47 MET cc_start: 0.1191 (ttp) cc_final: 0.0464 (ttm) REVERT: N 206 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6525 (ttm110) REVERT: N 305 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7728 (mmt) REVERT: N 328 LYS cc_start: 0.7427 (tptt) cc_final: 0.7042 (tptm) REVERT: N 360 GLN cc_start: 0.7495 (tm-30) cc_final: 0.7271 (tp-100) REVERT: O 68 LYS cc_start: 0.8021 (ptmt) cc_final: 0.7728 (ptpp) REVERT: O 100 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7695 (mt-10) REVERT: O 206 ARG cc_start: 0.7484 (ttp-170) cc_final: 0.6270 (ttm-80) REVERT: O 276 GLU cc_start: 0.7113 (tt0) cc_final: 0.6807 (tt0) REVERT: O 284 LYS cc_start: 0.8121 (mttm) cc_final: 0.7720 (mttm) REVERT: O 286 ASP cc_start: 0.6763 (t0) cc_final: 0.6448 (m-30) REVERT: O 326 LYS cc_start: 0.7552 (ptpp) cc_final: 0.6679 (mmmt) REVERT: O 328 LYS cc_start: 0.7745 (mtmt) cc_final: 0.6828 (tptm) REVERT: O 359 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7640 (tptp) REVERT: P 71 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7196 (mm) REVERT: P 82 MET cc_start: 0.7901 (tpt) cc_final: 0.7269 (tpt) REVERT: P 206 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6384 (ttp-110) REVERT: P 224 GLU cc_start: 0.7096 (tp30) cc_final: 0.6876 (mm-30) REVERT: P 241 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7436 (tp30) REVERT: P 355 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7789 (mtt) REVERT: P 359 LYS cc_start: 0.7296 (ptmm) cc_final: 0.6865 (tptt) REVERT: Q 6 THR cc_start: 0.8087 (p) cc_final: 0.7516 (t) REVERT: Q 34 ILE cc_start: 0.8419 (mt) cc_final: 0.8103 (pt) REVERT: Q 47 MET cc_start: 0.6551 (mmm) cc_final: 0.5451 (ptt) REVERT: Q 60 SER cc_start: 0.7818 (t) cc_final: 0.7581 (p) REVERT: Q 72 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6944 (mt-10) REVERT: Q 190 MET cc_start: 0.7418 (mtm) cc_final: 0.7038 (mtp) REVERT: Q 225 ASN cc_start: 0.7063 (t0) cc_final: 0.6596 (m110) REVERT: Q 286 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: Q 291 LYS cc_start: 0.5359 (mttm) cc_final: 0.4676 (tmtm) REVERT: Q 328 LYS cc_start: 0.7310 (ttmt) cc_final: 0.6502 (ttpp) REVERT: Q 336 LYS cc_start: 0.7737 (tptm) cc_final: 0.7361 (ttmt) REVERT: Q 354 GLN cc_start: 0.7647 (pm20) cc_final: 0.7280 (mm110) REVERT: R 37 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.5926 (mpp-170) REVERT: R 72 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7314 (mt-10) REVERT: R 99 GLU cc_start: 0.7299 (pt0) cc_final: 0.6977 (pm20) REVERT: R 206 ARG cc_start: 0.6804 (tpp80) cc_final: 0.6246 (ttm-80) REVERT: R 215 LYS cc_start: 0.7584 (mmmt) cc_final: 0.7347 (mptm) REVERT: R 225 ASN cc_start: 0.6583 (t0) cc_final: 0.6172 (m-40) REVERT: R 288 ASP cc_start: 0.7659 (p0) cc_final: 0.7453 (m-30) REVERT: R 314 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.6832 (tt0) outliers start: 137 outliers final: 64 residues processed: 683 average time/residue: 2.8220 time to fit residues: 2345.9465 Evaluate side-chains 659 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 573 time to evaluate : 4.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 336 LYS Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 71 ILE Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 241 GLU Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 286 ASP Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 314 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 393 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 351 optimal weight: 0.6980 chunk 195 optimal weight: 0.7980 chunk 403 optimal weight: 1.9990 chunk 326 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 424 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 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 98 GLN D 143 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN R 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 39895 Z= 0.237 Angle : 0.587 7.057 54139 Z= 0.292 Chirality : 0.044 0.176 5990 Planarity : 0.004 0.059 6962 Dihedral : 9.102 170.947 5563 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.93 % Allowed : 15.36 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.12), residues: 4854 helix: 0.01 (0.12), residues: 1978 sheet: -0.37 (0.16), residues: 931 loop : 0.65 (0.15), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 340 HIS 0.006 0.001 HIS O 161 PHE 0.016 0.001 PHE B 277 TYR 0.014 0.001 TYR F 8 ARG 0.008 0.000 ARG C 192 *********************** 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 713 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 590 time to evaluate : 4.836 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: A 100 GLU cc_start: 0.7313 (pt0) cc_final: 0.7016 (pp20) REVERT: A 137 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5852 (mp0) REVERT: A 207 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6672 (tppt) REVERT: A 239 ARG cc_start: 0.5905 (mtt180) cc_final: 0.5389 (mtm-85) REVERT: A 242 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.5935 (mp0) REVERT: A 253 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.6138 (mptt) REVERT: A 302 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6503 (m-30) REVERT: A 340 LYS cc_start: 0.7094 (tptp) cc_final: 0.6644 (ttpt) REVERT: A 406 LYS cc_start: 0.6885 (pttp) cc_final: 0.6511 (ptpt) REVERT: B 68 LYS cc_start: 0.6619 (mtmt) cc_final: 0.6173 (mtmt) REVERT: B 73 ASN cc_start: 0.7524 (m-40) cc_final: 0.7044 (t0) REVERT: B 75 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6761 (pt) REVERT: B 96 ILE cc_start: 0.7755 (mm) cc_final: 0.7319 (pt) REVERT: B 228 LYS cc_start: 0.6617 (ttpt) cc_final: 0.5892 (ttpp) REVERT: B 295 ARG cc_start: 0.6616 (mtp180) cc_final: 0.5564 (mpt-90) REVERT: B 364 ASN cc_start: 0.7335 (m-40) cc_final: 0.6750 (t0) REVERT: B 376 GLU cc_start: 0.7441 (pt0) cc_final: 0.6909 (pp20) REVERT: C 22 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7304 (mp10) REVERT: C 83 GLU cc_start: 0.7000 (tt0) cc_final: 0.6177 (mp0) REVERT: C 91 LYS cc_start: 0.7431 (ttpt) cc_final: 0.5897 (tptp) REVERT: C 242 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7349 (mtm-85) REVERT: C 251 GLN cc_start: 0.7331 (mt0) cc_final: 0.6878 (mp10) REVERT: C 359 ASN cc_start: 0.6752 (m110) cc_final: 0.6020 (t0) REVERT: D 13 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6190 (mt-10) REVERT: D 47 LYS cc_start: 0.7801 (mtmm) cc_final: 0.7281 (mttp) REVERT: D 73 GLN cc_start: 0.7217 (tt0) cc_final: 0.6994 (mt0) REVERT: D 84 MET cc_start: 0.7269 (mpp) cc_final: 0.7018 (tmm) REVERT: D 106 GLN cc_start: 0.6316 (pt0) cc_final: 0.5925 (mt0) REVERT: D 113 MET cc_start: 0.6788 (tpp) cc_final: 0.6578 (mmt) REVERT: D 172 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6454 (mt-10) REVERT: D 255 ARG cc_start: 0.5712 (mtm110) cc_final: 0.5207 (mtt90) REVERT: D 269 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6518 (mp) REVERT: D 287 ARG cc_start: 0.6108 (OUTLIER) cc_final: 0.5354 (mtp180) REVERT: E 58 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7351 (ptm160) REVERT: E 94 ARG cc_start: 0.7633 (mtp180) cc_final: 0.7133 (mtp180) REVERT: E 98 SER cc_start: 0.6970 (t) cc_final: 0.6571 (m) REVERT: E 115 ASN cc_start: 0.6505 (m-40) cc_final: 0.6295 (m-40) REVERT: F 23 GLU cc_start: 0.7586 (tt0) cc_final: 0.7216 (tt0) REVERT: F 58 GLN cc_start: 0.7448 (mp-120) cc_final: 0.6033 (tp-100) REVERT: F 81 GLU cc_start: 0.6737 (mp0) cc_final: 0.5799 (mm-30) REVERT: F 83 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6836 (mt-10) REVERT: F 97 ARG cc_start: 0.7322 (mmm160) cc_final: 0.6898 (mmm160) REVERT: F 107 LYS cc_start: 0.7071 (mmmm) cc_final: 0.6730 (mttt) REVERT: F 119 THR cc_start: 0.7361 (m) cc_final: 0.7049 (p) REVERT: F 145 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5354 (mm-30) REVERT: F 148 GLU cc_start: 0.6937 (tt0) cc_final: 0.6688 (tt0) REVERT: G 135 GLU cc_start: 0.6684 (tt0) cc_final: 0.6417 (tt0) REVERT: H 28 ARG cc_start: 0.7661 (tpp-160) cc_final: 0.7316 (tpp80) REVERT: H 45 VAL cc_start: 0.7684 (m) cc_final: 0.7479 (t) REVERT: H 68 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7423 (mttm) REVERT: H 72 GLU cc_start: 0.6995 (tt0) cc_final: 0.6576 (mp0) REVERT: H 141 SER cc_start: 0.7790 (t) cc_final: 0.7399 (m) REVERT: H 206 ARG cc_start: 0.6576 (ttm-80) cc_final: 0.5680 (ttm110) REVERT: H 225 ASN cc_start: 0.7566 (m-40) cc_final: 0.6881 (t0) REVERT: H 234 SER cc_start: 0.7221 (m) cc_final: 0.6894 (t) REVERT: H 306 TYR cc_start: 0.8838 (m-80) cc_final: 0.8528 (m-80) REVERT: H 328 LYS cc_start: 0.6882 (mmmm) cc_final: 0.6655 (mppt) REVERT: I 50 LYS cc_start: 0.7294 (mmpt) cc_final: 0.6933 (mtpt) REVERT: I 68 LYS cc_start: 0.8048 (mmmt) cc_final: 0.7466 (mttt) REVERT: I 152 VAL cc_start: 0.7303 (OUTLIER) cc_final: 0.7071 (t) REVERT: I 215 LYS cc_start: 0.7695 (mtpp) cc_final: 0.7325 (mttp) REVERT: I 305 MET cc_start: 0.8319 (mmm) cc_final: 0.7961 (mmm) REVERT: I 336 LYS cc_start: 0.6887 (ptpp) cc_final: 0.6432 (ttpt) REVERT: M 78 ASN cc_start: 0.7624 (t0) cc_final: 0.7213 (t0) REVERT: M 80 ASP cc_start: 0.6798 (OUTLIER) cc_final: 0.6574 (t70) REVERT: M 194 THR cc_start: 0.8150 (m) cc_final: 0.7759 (p) REVERT: M 202 THR cc_start: 0.7224 (m) cc_final: 0.6755 (p) REVERT: M 227 MET cc_start: 0.8404 (mmt) cc_final: 0.8136 (mmt) REVERT: M 263 GLN cc_start: 0.7721 (mt0) cc_final: 0.7431 (mt0) REVERT: N 47 MET cc_start: 0.1199 (ttp) cc_final: 0.0472 (ttm) REVERT: N 206 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6528 (ttm110) REVERT: N 211 ASP cc_start: 0.7579 (m-30) cc_final: 0.7329 (t70) REVERT: N 305 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7822 (mmt) REVERT: N 328 LYS cc_start: 0.7397 (tptt) cc_final: 0.6987 (tptm) REVERT: O 68 LYS cc_start: 0.7987 (ptmt) cc_final: 0.7681 (ptpp) REVERT: O 100 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7691 (mt-10) REVERT: O 176 MET cc_start: 0.8494 (mmm) cc_final: 0.8270 (mmm) REVERT: O 206 ARG cc_start: 0.7427 (ttp-170) cc_final: 0.6233 (ttm-80) REVERT: O 276 GLU cc_start: 0.7112 (tt0) cc_final: 0.6817 (tt0) REVERT: O 284 LYS cc_start: 0.8086 (mttm) cc_final: 0.7700 (mttm) REVERT: O 286 ASP cc_start: 0.6826 (t0) cc_final: 0.6490 (m-30) REVERT: O 326 LYS cc_start: 0.7505 (ptpp) cc_final: 0.6630 (mmmt) REVERT: O 328 LYS cc_start: 0.7747 (mtmt) cc_final: 0.6812 (tptm) REVERT: O 359 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7659 (tptp) REVERT: P 82 MET cc_start: 0.7899 (tpt) cc_final: 0.7258 (tpt) REVERT: P 224 GLU cc_start: 0.7157 (tp30) cc_final: 0.6922 (mm-30) REVERT: P 241 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: P 355 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7788 (mtt) REVERT: P 359 LYS cc_start: 0.7235 (ptmm) cc_final: 0.6799 (tptt) REVERT: Q 34 ILE cc_start: 0.8413 (mt) cc_final: 0.8119 (pt) REVERT: Q 47 MET cc_start: 0.6612 (mmm) cc_final: 0.5514 (ptt) REVERT: Q 60 SER cc_start: 0.7761 (t) cc_final: 0.7452 (p) REVERT: Q 61 LYS cc_start: 0.7589 (mtpp) cc_final: 0.7107 (mttp) REVERT: Q 72 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6946 (mt-10) REVERT: Q 190 MET cc_start: 0.7362 (mtm) cc_final: 0.6979 (mtp) REVERT: Q 225 ASN cc_start: 0.7103 (t0) cc_final: 0.6604 (m110) REVERT: Q 286 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: Q 291 LYS cc_start: 0.5309 (mttm) cc_final: 0.4649 (tmtm) REVERT: Q 313 MET cc_start: 0.7934 (tpt) cc_final: 0.7488 (mmm) REVERT: Q 328 LYS cc_start: 0.7321 (ttmt) cc_final: 0.6565 (ttmt) REVERT: Q 336 LYS cc_start: 0.7727 (tptm) cc_final: 0.7344 (ttmt) REVERT: Q 354 GLN cc_start: 0.7592 (pm20) cc_final: 0.7244 (mm110) REVERT: R 37 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.5901 (mpp-170) REVERT: R 72 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7291 (mt-10) REVERT: R 99 GLU cc_start: 0.7376 (pt0) cc_final: 0.7074 (pm20) REVERT: R 206 ARG cc_start: 0.6776 (tpp80) cc_final: 0.6142 (ttm-80) REVERT: R 215 LYS cc_start: 0.7546 (mmmt) cc_final: 0.7208 (mmtm) REVERT: R 225 ASN cc_start: 0.6576 (t0) cc_final: 0.6155 (m-40) outliers start: 123 outliers final: 62 residues processed: 671 average time/residue: 2.8573 time to fit residues: 2336.2680 Evaluate side-chains 645 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 561 time to evaluate : 5.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 336 LYS Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 71 ILE Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 241 GLU Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 147 ARG Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 286 ASP Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 152 VAL 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: 5.9990 chunk 425 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 277 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 473 optimal weight: 2.9990 chunk 392 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 156 optimal weight: 0.4980 chunk 248 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 143 ASN D 254 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 59 GLN N 360 GLN O 225 ASN R 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 39895 Z= 0.196 Angle : 0.564 6.543 54139 Z= 0.278 Chirality : 0.043 0.160 5990 Planarity : 0.004 0.084 6962 Dihedral : 8.638 177.999 5553 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.29 % Allowed : 16.27 % Favored : 81.44 % 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: 0.28 (0.12), residues: 4854 helix: 0.22 (0.12), residues: 1978 sheet: -0.34 (0.16), residues: 931 loop : 0.73 (0.15), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 102 HIS 0.005 0.001 HIS O 161 PHE 0.014 0.001 PHE B 277 TYR 0.014 0.001 TYR F 8 ARG 0.010 0.000 ARG C 192 *********************** 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 678 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 582 time to evaluate : 5.064 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: A 100 GLU cc_start: 0.7308 (pt0) cc_final: 0.7013 (pp20) REVERT: A 137 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5843 (mp0) REVERT: A 204 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7540 (p) REVERT: A 207 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6670 (tppt) REVERT: A 239 ARG cc_start: 0.5813 (mtt180) cc_final: 0.5300 (mtm-85) REVERT: A 242 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.5919 (mp0) REVERT: A 253 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.6130 (mptt) REVERT: A 302 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6550 (m-30) REVERT: A 340 LYS cc_start: 0.7058 (tptp) cc_final: 0.6608 (ttpt) REVERT: A 406 LYS cc_start: 0.6902 (pttp) cc_final: 0.6509 (ptpt) REVERT: B 68 LYS cc_start: 0.6600 (mtmt) cc_final: 0.6189 (mtmt) REVERT: B 73 ASN cc_start: 0.7554 (m-40) cc_final: 0.7082 (t0) REVERT: B 75 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6824 (pt) REVERT: B 96 ILE cc_start: 0.7870 (mm) cc_final: 0.7395 (pt) REVERT: B 149 SER cc_start: 0.8382 (p) cc_final: 0.8181 (t) REVERT: B 228 LYS cc_start: 0.6590 (ttpt) cc_final: 0.5862 (ttpp) REVERT: B 295 ARG cc_start: 0.6585 (mtp180) cc_final: 0.5546 (mpt-90) REVERT: B 364 ASN cc_start: 0.7294 (m-40) cc_final: 0.6717 (t0) REVERT: B 376 GLU cc_start: 0.7435 (pt0) cc_final: 0.6892 (pp20) REVERT: C 22 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7322 (mp10) REVERT: C 83 GLU cc_start: 0.7002 (tt0) cc_final: 0.6181 (mp0) REVERT: C 91 LYS cc_start: 0.7464 (ttpt) cc_final: 0.5936 (tptp) REVERT: C 93 THR cc_start: 0.8042 (m) cc_final: 0.7837 (m) REVERT: C 251 GLN cc_start: 0.7319 (mt0) cc_final: 0.6887 (mp10) REVERT: C 359 ASN cc_start: 0.6763 (m110) cc_final: 0.6015 (t0) REVERT: D 13 GLU cc_start: 0.6572 (mm-30) cc_final: 0.6145 (mt-10) REVERT: D 47 LYS cc_start: 0.7708 (mtmm) cc_final: 0.7186 (mttp) REVERT: D 73 GLN cc_start: 0.7206 (tt0) cc_final: 0.6985 (mt0) REVERT: D 84 MET cc_start: 0.7263 (mpp) cc_final: 0.7012 (tmm) REVERT: D 106 GLN cc_start: 0.6253 (pt0) cc_final: 0.5934 (mt0) REVERT: D 172 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6476 (mt-10) REVERT: D 221 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6860 (m-30) REVERT: D 255 ARG cc_start: 0.5751 (mtm110) cc_final: 0.5210 (mtt90) REVERT: D 269 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6491 (mp) REVERT: D 287 ARG cc_start: 0.6099 (OUTLIER) cc_final: 0.5491 (mtp180) REVERT: E 61 GLU cc_start: 0.7068 (tt0) cc_final: 0.6588 (mt-10) REVERT: E 94 ARG cc_start: 0.7610 (mtp180) cc_final: 0.7138 (mtp180) REVERT: E 98 SER cc_start: 0.6886 (t) cc_final: 0.6518 (m) REVERT: E 115 ASN cc_start: 0.6396 (m-40) cc_final: 0.6193 (m-40) REVERT: F 23 GLU cc_start: 0.7525 (tt0) cc_final: 0.7184 (tt0) REVERT: F 58 GLN cc_start: 0.7399 (mp-120) cc_final: 0.5979 (tp-100) REVERT: F 81 GLU cc_start: 0.6795 (mp0) cc_final: 0.5792 (mm-30) REVERT: F 97 ARG cc_start: 0.7285 (mmm160) cc_final: 0.6844 (mmm160) REVERT: F 107 LYS cc_start: 0.7045 (mmmm) cc_final: 0.6655 (mttt) REVERT: F 119 THR cc_start: 0.7303 (m) cc_final: 0.7004 (p) REVERT: F 145 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.5385 (mm-30) REVERT: G 135 GLU cc_start: 0.6633 (tt0) cc_final: 0.6386 (tt0) REVERT: H 28 ARG cc_start: 0.7667 (tpp-160) cc_final: 0.7327 (tpp80) REVERT: H 45 VAL cc_start: 0.7666 (m) cc_final: 0.7461 (t) REVERT: H 68 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7416 (mttm) REVERT: H 72 GLU cc_start: 0.7034 (tt0) cc_final: 0.6597 (mp0) REVERT: H 141 SER cc_start: 0.7767 (t) cc_final: 0.7364 (m) REVERT: H 206 ARG cc_start: 0.6592 (ttm-80) cc_final: 0.5698 (ttm110) REVERT: H 225 ASN cc_start: 0.7537 (m-40) cc_final: 0.6814 (t0) REVERT: H 234 SER cc_start: 0.7198 (m) cc_final: 0.6864 (t) REVERT: H 306 TYR cc_start: 0.8823 (m-80) cc_final: 0.8534 (m-80) REVERT: H 328 LYS cc_start: 0.6919 (mmmm) cc_final: 0.6704 (mppt) REVERT: I 50 LYS cc_start: 0.7289 (mmpt) cc_final: 0.6909 (mtpt) REVERT: I 68 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7477 (mttt) REVERT: I 152 VAL cc_start: 0.7267 (OUTLIER) cc_final: 0.7033 (t) REVERT: I 180 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7054 (tt) REVERT: I 215 LYS cc_start: 0.7705 (mtpp) cc_final: 0.7329 (mttp) REVERT: I 305 MET cc_start: 0.8327 (mmm) cc_final: 0.7980 (mmm) REVERT: I 336 LYS cc_start: 0.6876 (ptpp) cc_final: 0.6393 (ttpt) REVERT: M 78 ASN cc_start: 0.7618 (t0) cc_final: 0.7199 (t0) REVERT: M 194 THR cc_start: 0.8151 (m) cc_final: 0.7789 (p) REVERT: M 196 ARG cc_start: 0.7807 (mmt90) cc_final: 0.7601 (mmt90) REVERT: M 202 THR cc_start: 0.7103 (m) cc_final: 0.6593 (p) REVERT: M 206 ARG cc_start: 0.7606 (ttp80) cc_final: 0.7147 (mtp-110) REVERT: M 227 MET cc_start: 0.8419 (mmt) cc_final: 0.8121 (mmt) REVERT: N 47 MET cc_start: 0.1187 (ttp) cc_final: 0.0475 (ttm) REVERT: N 211 ASP cc_start: 0.7574 (m-30) cc_final: 0.7327 (t70) REVERT: N 225 ASN cc_start: 0.7140 (t0) cc_final: 0.6710 (m-40) REVERT: N 305 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7713 (mmt) REVERT: N 328 LYS cc_start: 0.7461 (tptt) cc_final: 0.7063 (tptm) REVERT: O 68 LYS cc_start: 0.7987 (ptmt) cc_final: 0.7668 (ptpp) REVERT: O 100 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7693 (mt-10) REVERT: O 206 ARG cc_start: 0.7405 (ttp-170) cc_final: 0.6202 (ttm-80) REVERT: O 276 GLU cc_start: 0.7108 (tt0) cc_final: 0.6836 (tt0) REVERT: O 284 LYS cc_start: 0.8065 (mttm) cc_final: 0.7638 (mttm) REVERT: O 286 ASP cc_start: 0.6832 (t0) cc_final: 0.6520 (m-30) REVERT: O 326 LYS cc_start: 0.7487 (ptpp) cc_final: 0.6608 (mmmt) REVERT: O 328 LYS cc_start: 0.7737 (mtmt) cc_final: 0.6792 (tptm) REVERT: O 359 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7642 (tptp) REVERT: P 82 MET cc_start: 0.7896 (tpt) cc_final: 0.7307 (tpt) REVERT: P 206 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6301 (ttm110) REVERT: P 355 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8029 (mpp) REVERT: P 359 LYS cc_start: 0.7224 (ptmm) cc_final: 0.6794 (tptt) REVERT: Q 34 ILE cc_start: 0.8401 (mt) cc_final: 0.8120 (pt) REVERT: Q 47 MET cc_start: 0.6642 (mmm) cc_final: 0.5588 (ptt) REVERT: Q 60 SER cc_start: 0.7728 (t) cc_final: 0.7430 (p) REVERT: Q 61 LYS cc_start: 0.7561 (mtpp) cc_final: 0.7096 (mtpp) REVERT: Q 72 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6908 (mt-10) REVERT: Q 190 MET cc_start: 0.7373 (mtm) cc_final: 0.7007 (mtp) REVERT: Q 225 ASN cc_start: 0.7104 (t0) cc_final: 0.6597 (m110) REVERT: Q 291 LYS cc_start: 0.5374 (mttm) cc_final: 0.4709 (tmtm) REVERT: Q 313 MET cc_start: 0.7924 (tpt) cc_final: 0.7637 (mmm) REVERT: Q 328 LYS cc_start: 0.7282 (ttmt) cc_final: 0.6528 (ttmt) REVERT: Q 336 LYS cc_start: 0.7722 (tptm) cc_final: 0.7353 (ttmt) REVERT: Q 354 GLN cc_start: 0.7562 (pm20) cc_final: 0.7251 (mm110) REVERT: R 37 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.5895 (mpp-170) REVERT: R 72 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7357 (mt-10) REVERT: R 99 GLU cc_start: 0.7385 (pt0) cc_final: 0.7121 (pm20) REVERT: R 206 ARG cc_start: 0.6754 (tpp80) cc_final: 0.6121 (ttm-80) REVERT: R 215 LYS cc_start: 0.7536 (mmmt) cc_final: 0.7195 (mmtm) REVERT: R 225 ASN cc_start: 0.6562 (t0) cc_final: 0.6144 (m-40) REVERT: R 358 THR cc_start: 0.7625 (m) cc_final: 0.7367 (p) outliers start: 96 outliers final: 54 residues processed: 645 average time/residue: 2.8364 time to fit residues: 2229.6628 Evaluate side-chains 642 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 568 time to evaluate : 4.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 336 LYS Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 147 ARG Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 247 VAL 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: 5.9990 chunk 269 optimal weight: 4.9990 chunk 345 optimal weight: 5.9990 chunk 267 optimal weight: 9.9990 chunk 398 optimal weight: 0.9990 chunk 264 optimal weight: 0.9990 chunk 471 optimal weight: 3.9990 chunk 294 optimal weight: 0.6980 chunk 287 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 227 HIS D 143 ASN D 160 HIS ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN ** I 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN R 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 39895 Z= 0.313 Angle : 0.601 7.541 54139 Z= 0.299 Chirality : 0.045 0.173 5990 Planarity : 0.005 0.075 6962 Dihedral : 8.659 175.207 5551 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.98 % Allowed : 16.17 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.12), residues: 4854 helix: 0.16 (0.12), residues: 1978 sheet: -0.20 (0.17), residues: 851 loop : 0.55 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 340 HIS 0.007 0.001 HIS A 404 PHE 0.017 0.001 PHE F 101 TYR 0.015 0.001 TYR I 279 ARG 0.011 0.000 ARG F 42 *********************** 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 710 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 585 time to evaluate : 4.912 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: A 70 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6485 (mm-30) REVERT: A 100 GLU cc_start: 0.7325 (pt0) cc_final: 0.7011 (pp20) REVERT: A 137 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5852 (mp0) REVERT: A 204 SER cc_start: 0.7846 (OUTLIER) cc_final: 0.7595 (p) REVERT: A 207 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6666 (tppt) REVERT: A 239 ARG cc_start: 0.5837 (mtt180) cc_final: 0.5330 (mtm-85) REVERT: A 242 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.5958 (mp0) REVERT: A 253 LYS cc_start: 0.6563 (OUTLIER) cc_final: 0.6153 (mptt) REVERT: A 302 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6618 (m-30) REVERT: A 340 LYS cc_start: 0.7047 (tptp) cc_final: 0.6591 (ttpt) REVERT: A 406 LYS cc_start: 0.6959 (pttp) cc_final: 0.6525 (ptpt) REVERT: B 21 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7416 (mtmm) REVERT: B 68 LYS cc_start: 0.6658 (mtmt) cc_final: 0.6280 (mtmt) REVERT: B 72 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7222 (tp30) REVERT: B 73 ASN cc_start: 0.7600 (m-40) cc_final: 0.7152 (t0) REVERT: B 75 ILE cc_start: 0.7021 (OUTLIER) cc_final: 0.6749 (pt) REVERT: B 96 ILE cc_start: 0.7859 (mm) cc_final: 0.7392 (pt) REVERT: B 228 LYS cc_start: 0.6621 (ttpt) cc_final: 0.5876 (ttpp) REVERT: B 295 ARG cc_start: 0.6684 (mtp180) cc_final: 0.5558 (mpt-90) REVERT: B 364 ASN cc_start: 0.7317 (m-40) cc_final: 0.6731 (t0) REVERT: B 376 GLU cc_start: 0.7464 (pt0) cc_final: 0.6915 (pp20) REVERT: C 22 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7304 (mp10) REVERT: C 83 GLU cc_start: 0.6978 (tt0) cc_final: 0.6175 (mp0) REVERT: C 91 LYS cc_start: 0.7503 (ttpt) cc_final: 0.6058 (tttt) REVERT: C 251 GLN cc_start: 0.7380 (mt0) cc_final: 0.6982 (mp10) REVERT: C 359 ASN cc_start: 0.6827 (m110) cc_final: 0.6121 (t0) REVERT: D 13 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6191 (mt-10) REVERT: D 47 LYS cc_start: 0.7703 (mtmm) cc_final: 0.7170 (mttp) REVERT: D 73 GLN cc_start: 0.7198 (tt0) cc_final: 0.6976 (mt0) REVERT: D 84 MET cc_start: 0.7276 (mpp) cc_final: 0.7050 (tmm) REVERT: D 102 GLU cc_start: 0.6505 (mp0) cc_final: 0.6138 (mp0) REVERT: D 106 GLN cc_start: 0.6191 (pt0) cc_final: 0.5953 (mt0) REVERT: D 172 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6598 (mt-10) REVERT: D 221 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6858 (m-30) REVERT: D 255 ARG cc_start: 0.5861 (mtm110) cc_final: 0.5310 (mtt90) REVERT: D 269 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6507 (mp) REVERT: D 287 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.5476 (mtp180) REVERT: E 98 SER cc_start: 0.6889 (t) cc_final: 0.6494 (m) REVERT: F 23 GLU cc_start: 0.7596 (tt0) cc_final: 0.7222 (tt0) REVERT: F 58 GLN cc_start: 0.7436 (mp-120) cc_final: 0.6149 (tp-100) REVERT: F 81 GLU cc_start: 0.6836 (mp0) cc_final: 0.5867 (mm-30) REVERT: F 83 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6646 (mt-10) REVERT: F 97 ARG cc_start: 0.7336 (mmm160) cc_final: 0.6887 (mmm160) REVERT: F 107 LYS cc_start: 0.7080 (mmmm) cc_final: 0.6746 (mttt) REVERT: F 110 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7416 (tm130) REVERT: F 119 THR cc_start: 0.7362 (m) cc_final: 0.7075 (p) REVERT: F 145 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5439 (mm-30) REVERT: G 135 GLU cc_start: 0.6688 (tt0) cc_final: 0.6440 (tt0) REVERT: H 28 ARG cc_start: 0.7675 (tpp-160) cc_final: 0.7358 (tpp80) REVERT: H 45 VAL cc_start: 0.7704 (m) cc_final: 0.7479 (t) REVERT: H 68 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7445 (mttm) REVERT: H 72 GLU cc_start: 0.7084 (tt0) cc_final: 0.6605 (mp0) REVERT: H 141 SER cc_start: 0.7818 (t) cc_final: 0.7411 (m) REVERT: H 165 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7352 (mt) REVERT: H 206 ARG cc_start: 0.6646 (ttm-80) cc_final: 0.6094 (ttp-170) REVERT: H 225 ASN cc_start: 0.7558 (m-40) cc_final: 0.6835 (t0) REVERT: H 234 SER cc_start: 0.7199 (m) cc_final: 0.6872 (t) REVERT: H 306 TYR cc_start: 0.8857 (m-80) cc_final: 0.8566 (m-80) REVERT: H 328 LYS cc_start: 0.6957 (mmmm) cc_final: 0.6729 (mppt) REVERT: I 50 LYS cc_start: 0.7300 (mmpt) cc_final: 0.6889 (mtpm) REVERT: I 68 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7496 (mttt) REVERT: I 152 VAL cc_start: 0.7258 (OUTLIER) cc_final: 0.6996 (t) REVERT: I 180 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7054 (tt) REVERT: I 215 LYS cc_start: 0.7698 (mtpp) cc_final: 0.7322 (mttp) REVERT: I 305 MET cc_start: 0.8355 (mmm) cc_final: 0.7861 (mmm) REVERT: I 336 LYS cc_start: 0.6962 (ptpp) cc_final: 0.6485 (ttpt) REVERT: M 52 SER cc_start: 0.7142 (p) cc_final: 0.6867 (m) REVERT: M 66 THR cc_start: 0.7588 (m) cc_final: 0.7260 (p) REVERT: M 78 ASN cc_start: 0.7604 (t0) cc_final: 0.7155 (t0) REVERT: M 83 GLU cc_start: 0.7104 (tt0) cc_final: 0.6499 (tm-30) REVERT: M 194 THR cc_start: 0.8190 (m) cc_final: 0.7863 (p) REVERT: M 202 THR cc_start: 0.7259 (m) cc_final: 0.6777 (p) REVERT: N 47 MET cc_start: 0.1004 (ttp) cc_final: 0.0314 (ttm) REVERT: N 206 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6511 (ttm110) REVERT: N 211 ASP cc_start: 0.7621 (m-30) cc_final: 0.7274 (t70) REVERT: N 236 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7622 (mp) REVERT: N 297 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7897 (m110) REVERT: N 305 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7797 (mmt) REVERT: N 328 LYS cc_start: 0.7488 (tptt) cc_final: 0.7048 (tptm) REVERT: O 68 LYS cc_start: 0.8002 (ptmt) cc_final: 0.7677 (ptpp) REVERT: O 100 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7746 (mt-10) REVERT: O 206 ARG cc_start: 0.7486 (ttp-170) cc_final: 0.6260 (ttm-80) REVERT: O 276 GLU cc_start: 0.7099 (tt0) cc_final: 0.6832 (tt0) REVERT: O 284 LYS cc_start: 0.8144 (mttm) cc_final: 0.7702 (mttm) REVERT: O 286 ASP cc_start: 0.6821 (t0) cc_final: 0.6500 (m-30) REVERT: O 326 LYS cc_start: 0.7627 (ptpp) cc_final: 0.6808 (mmmt) REVERT: O 328 LYS cc_start: 0.7697 (mtmt) cc_final: 0.6983 (mttp) REVERT: O 359 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7639 (tptp) REVERT: P 82 MET cc_start: 0.7915 (tpt) cc_final: 0.7358 (tpt) REVERT: P 206 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6224 (ttm110) REVERT: P 355 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7992 (mpp) REVERT: P 359 LYS cc_start: 0.7264 (ptmm) cc_final: 0.6839 (tptt) REVERT: Q 34 ILE cc_start: 0.8403 (mt) cc_final: 0.8079 (pt) REVERT: Q 47 MET cc_start: 0.6766 (mmm) cc_final: 0.5600 (ptt) REVERT: Q 60 SER cc_start: 0.7753 (t) cc_final: 0.7435 (p) REVERT: Q 61 LYS cc_start: 0.7643 (mtpp) cc_final: 0.7206 (mtpp) REVERT: Q 72 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6965 (mt-10) REVERT: Q 190 MET cc_start: 0.7404 (mtm) cc_final: 0.7033 (mtp) REVERT: Q 225 ASN cc_start: 0.7105 (t0) cc_final: 0.6613 (m110) REVERT: Q 286 ASP cc_start: 0.7911 (m-30) cc_final: 0.7668 (m-30) REVERT: Q 291 LYS cc_start: 0.5380 (mttm) cc_final: 0.4716 (tmtm) REVERT: Q 313 MET cc_start: 0.7978 (tpt) cc_final: 0.7547 (mmm) REVERT: Q 328 LYS cc_start: 0.7326 (ttmt) cc_final: 0.6571 (ttmt) REVERT: Q 336 LYS cc_start: 0.7759 (tptm) cc_final: 0.7438 (ttmt) REVERT: Q 354 GLN cc_start: 0.7610 (pm20) cc_final: 0.7242 (mm110) REVERT: R 37 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.5800 (mpp-170) REVERT: R 72 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7329 (mt-10) REVERT: R 99 GLU cc_start: 0.7379 (pt0) cc_final: 0.7092 (pm20) REVERT: R 206 ARG cc_start: 0.6808 (tpp80) cc_final: 0.6237 (ttm-80) REVERT: R 215 LYS cc_start: 0.7538 (mmmt) cc_final: 0.7204 (mmtm) REVERT: R 225 ASN cc_start: 0.6601 (t0) cc_final: 0.6146 (m-40) REVERT: R 358 THR cc_start: 0.7626 (m) cc_final: 0.7286 (p) outliers start: 125 outliers final: 73 residues processed: 673 average time/residue: 2.8126 time to fit residues: 2310.1593 Evaluate side-chains 660 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 562 time to evaluate : 4.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 297 ASN Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 336 LYS Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 71 ILE Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 291 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 281 optimal weight: 0.3980 chunk 141 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 chunk 321 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 370 optimal weight: 4.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 143 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 39895 Z= 0.362 Angle : 0.618 7.970 54139 Z= 0.309 Chirality : 0.046 0.179 5990 Planarity : 0.005 0.092 6962 Dihedral : 8.706 175.333 5550 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.93 % Allowed : 16.63 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.12), residues: 4854 helix: 0.06 (0.12), residues: 1978 sheet: -0.26 (0.17), residues: 856 loop : 0.47 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 340 HIS 0.007 0.001 HIS A 404 PHE 0.018 0.002 PHE F 101 TYR 0.017 0.001 TYR I 279 ARG 0.011 0.001 ARG F 42 *********************** 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 687 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 564 time to evaluate : 4.740 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: A 70 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6568 (mm-30) REVERT: A 100 GLU cc_start: 0.7325 (pt0) cc_final: 0.7005 (pp20) REVERT: A 137 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5836 (mp0) REVERT: A 204 SER cc_start: 0.7843 (OUTLIER) cc_final: 0.7612 (p) REVERT: A 207 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7108 (mmtp) REVERT: A 239 ARG cc_start: 0.5850 (mtt180) cc_final: 0.5354 (mtm-85) REVERT: A 242 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6007 (mp0) REVERT: A 253 LYS cc_start: 0.6580 (OUTLIER) cc_final: 0.6163 (mptt) REVERT: A 302 ASP cc_start: 0.7029 (OUTLIER) cc_final: 0.6649 (m-30) REVERT: A 340 LYS cc_start: 0.7034 (tptp) cc_final: 0.6571 (ttpt) REVERT: A 406 LYS cc_start: 0.6969 (pttp) cc_final: 0.6573 (ptpt) REVERT: B 21 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7469 (mtmm) REVERT: B 68 LYS cc_start: 0.6633 (mtmt) cc_final: 0.6251 (mtmt) REVERT: B 72 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7268 (tp30) REVERT: B 73 ASN cc_start: 0.7636 (m-40) cc_final: 0.7184 (t0) REVERT: B 75 ILE cc_start: 0.7032 (OUTLIER) cc_final: 0.6757 (pt) REVERT: B 96 ILE cc_start: 0.7843 (mm) cc_final: 0.7458 (pt) REVERT: B 228 LYS cc_start: 0.6653 (ttpt) cc_final: 0.5917 (ttpp) REVERT: B 295 ARG cc_start: 0.6672 (mtp180) cc_final: 0.5556 (mpt-90) REVERT: B 364 ASN cc_start: 0.7348 (m-40) cc_final: 0.6751 (t0) REVERT: C 22 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7310 (mp10) REVERT: C 83 GLU cc_start: 0.7018 (tt0) cc_final: 0.6189 (mp0) REVERT: C 91 LYS cc_start: 0.7503 (ttpt) cc_final: 0.6130 (tttt) REVERT: C 242 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7664 (ttm-80) REVERT: C 251 GLN cc_start: 0.7393 (mt0) cc_final: 0.6992 (mp10) REVERT: C 359 ASN cc_start: 0.6789 (m110) cc_final: 0.6073 (t0) REVERT: D 13 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6210 (mt-10) REVERT: D 47 LYS cc_start: 0.7692 (mtmm) cc_final: 0.7160 (mttp) REVERT: D 73 GLN cc_start: 0.7238 (tt0) cc_final: 0.7015 (mt0) REVERT: D 84 MET cc_start: 0.7274 (mpp) cc_final: 0.7066 (tmm) REVERT: D 172 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6670 (mt-10) REVERT: D 221 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6802 (m-30) REVERT: D 255 ARG cc_start: 0.5930 (mtm110) cc_final: 0.5338 (mtt90) REVERT: D 269 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6572 (mp) REVERT: D 287 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5555 (mtp180) REVERT: E 61 GLU cc_start: 0.7111 (tt0) cc_final: 0.6769 (mt-10) REVERT: E 94 ARG cc_start: 0.7633 (mtp180) cc_final: 0.7113 (mtp180) REVERT: E 98 SER cc_start: 0.6909 (t) cc_final: 0.6503 (m) REVERT: F 23 GLU cc_start: 0.7625 (tt0) cc_final: 0.7299 (tt0) REVERT: F 58 GLN cc_start: 0.7401 (mp-120) cc_final: 0.6140 (tp-100) REVERT: F 74 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7417 (mt) REVERT: F 81 GLU cc_start: 0.6907 (mp0) cc_final: 0.5974 (mm-30) REVERT: F 97 ARG cc_start: 0.7362 (mmm160) cc_final: 0.6910 (mmm160) REVERT: F 107 LYS cc_start: 0.7139 (mmmm) cc_final: 0.6790 (mttt) REVERT: F 110 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7469 (tm130) REVERT: F 119 THR cc_start: 0.7376 (m) cc_final: 0.7092 (p) REVERT: F 145 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.5439 (mm-30) REVERT: G 135 GLU cc_start: 0.6688 (tt0) cc_final: 0.6446 (tt0) REVERT: H 28 ARG cc_start: 0.7675 (tpp-160) cc_final: 0.7368 (tpp80) REVERT: H 45 VAL cc_start: 0.7715 (m) cc_final: 0.7510 (t) REVERT: H 68 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7455 (mttm) REVERT: H 72 GLU cc_start: 0.7055 (tt0) cc_final: 0.6575 (mp0) REVERT: H 141 SER cc_start: 0.7805 (t) cc_final: 0.7407 (m) REVERT: H 225 ASN cc_start: 0.7585 (m-40) cc_final: 0.6852 (t0) REVERT: H 234 SER cc_start: 0.7280 (m) cc_final: 0.6954 (t) REVERT: H 306 TYR cc_start: 0.8881 (m-80) cc_final: 0.8524 (m-80) REVERT: H 328 LYS cc_start: 0.6916 (mmmm) cc_final: 0.6668 (mppt) REVERT: I 50 LYS cc_start: 0.7312 (mmpt) cc_final: 0.6884 (mtpm) REVERT: I 68 LYS cc_start: 0.8079 (mmmt) cc_final: 0.7493 (mttt) REVERT: I 152 VAL cc_start: 0.7246 (OUTLIER) cc_final: 0.7029 (p) REVERT: I 180 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7086 (tt) REVERT: I 215 LYS cc_start: 0.7682 (mtpp) cc_final: 0.7291 (mttp) REVERT: I 305 MET cc_start: 0.8363 (mmm) cc_final: 0.7903 (mmm) REVERT: M 66 THR cc_start: 0.7659 (m) cc_final: 0.7361 (p) REVERT: M 78 ASN cc_start: 0.7621 (t0) cc_final: 0.7159 (t0) REVERT: M 194 THR cc_start: 0.8232 (m) cc_final: 0.7941 (p) REVERT: M 202 THR cc_start: 0.7373 (m) cc_final: 0.7012 (p) REVERT: N 47 MET cc_start: 0.0985 (ttp) cc_final: 0.0299 (ttm) REVERT: N 206 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6510 (ttm110) REVERT: N 211 ASP cc_start: 0.7651 (m-30) cc_final: 0.7379 (t70) REVERT: N 297 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7937 (m110) REVERT: N 305 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7822 (mmt) REVERT: N 328 LYS cc_start: 0.7488 (tptt) cc_final: 0.7029 (tptm) REVERT: O 68 LYS cc_start: 0.7988 (ptmt) cc_final: 0.7459 (mtpp) REVERT: O 100 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7763 (mt-10) REVERT: O 176 MET cc_start: 0.8502 (mmm) cc_final: 0.8269 (mmm) REVERT: O 206 ARG cc_start: 0.7495 (ttp-170) cc_final: 0.6282 (ttm-80) REVERT: O 276 GLU cc_start: 0.7112 (tt0) cc_final: 0.6829 (tt0) REVERT: O 284 LYS cc_start: 0.8120 (mttm) cc_final: 0.7672 (mttm) REVERT: O 286 ASP cc_start: 0.6798 (t0) cc_final: 0.6490 (m-30) REVERT: O 326 LYS cc_start: 0.7631 (ptpp) cc_final: 0.6878 (mmmt) REVERT: O 328 LYS cc_start: 0.7691 (mtmt) cc_final: 0.6948 (mttp) REVERT: O 359 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7655 (tptp) REVERT: P 82 MET cc_start: 0.7897 (tpt) cc_final: 0.7315 (tpt) REVERT: P 206 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6290 (ttm110) REVERT: P 355 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7922 (mpp) REVERT: P 359 LYS cc_start: 0.7282 (ptmm) cc_final: 0.6854 (tptt) REVERT: Q 34 ILE cc_start: 0.8417 (mt) cc_final: 0.8041 (pt) REVERT: Q 47 MET cc_start: 0.6842 (mmm) cc_final: 0.5612 (ptt) REVERT: Q 60 SER cc_start: 0.7752 (t) cc_final: 0.7431 (p) REVERT: Q 72 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7010 (mt-10) REVERT: Q 190 MET cc_start: 0.7425 (mtm) cc_final: 0.7129 (mtp) REVERT: Q 225 ASN cc_start: 0.7097 (t0) cc_final: 0.6623 (m110) REVERT: Q 286 ASP cc_start: 0.7910 (m-30) cc_final: 0.7666 (m-30) REVERT: Q 291 LYS cc_start: 0.5376 (mttm) cc_final: 0.4729 (tmtm) REVERT: Q 313 MET cc_start: 0.8015 (tpt) cc_final: 0.7576 (mmm) REVERT: Q 328 LYS cc_start: 0.7307 (ttmt) cc_final: 0.6565 (ttmt) REVERT: Q 336 LYS cc_start: 0.7786 (tptm) cc_final: 0.7436 (ttmt) REVERT: Q 354 GLN cc_start: 0.7612 (pm20) cc_final: 0.7233 (mm110) REVERT: R 37 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.5818 (mpp-170) REVERT: R 72 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7329 (mt-10) REVERT: R 99 GLU cc_start: 0.7389 (pt0) cc_final: 0.7111 (pm20) REVERT: R 206 ARG cc_start: 0.6836 (tpp80) cc_final: 0.6242 (ttm-80) REVERT: R 215 LYS cc_start: 0.7569 (mmmt) cc_final: 0.7238 (mmtm) REVERT: R 225 ASN cc_start: 0.6588 (t0) cc_final: 0.6143 (m-40) REVERT: R 358 THR cc_start: 0.7638 (m) cc_final: 0.7305 (p) outliers start: 123 outliers final: 74 residues processed: 652 average time/residue: 2.9515 time to fit residues: 2365.9476 Evaluate side-chains 660 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 561 time to evaluate : 4.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 297 ASN Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 336 LYS Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 71 ILE Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 348 SER Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain R residue 247 VAL 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: 1.9990 chunk 411 optimal weight: 3.9990 chunk 439 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 344 optimal weight: 0.5980 chunk 134 optimal weight: 0.8980 chunk 396 optimal weight: 1.9990 chunk 415 optimal weight: 3.9990 chunk 437 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 143 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN ** I 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN R 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39895 Z= 0.221 Angle : 0.571 7.129 54139 Z= 0.282 Chirality : 0.043 0.159 5990 Planarity : 0.005 0.085 6962 Dihedral : 8.404 169.281 5550 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.55 % Allowed : 16.87 % Favored : 80.59 % 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: 0.26 (0.12), residues: 4854 helix: 0.25 (0.12), residues: 1978 sheet: -0.22 (0.17), residues: 855 loop : 0.54 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 340 HIS 0.009 0.001 HIS I 173 PHE 0.014 0.001 PHE F 101 TYR 0.014 0.001 TYR F 8 ARG 0.014 0.000 ARG H 206 *********************** 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 685 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 578 time to evaluate : 4.784 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 100 GLU cc_start: 0.7319 (pt0) cc_final: 0.6987 (pp20) REVERT: A 137 GLU cc_start: 0.6192 (OUTLIER) cc_final: 0.5863 (mp0) REVERT: A 204 SER cc_start: 0.7863 (OUTLIER) cc_final: 0.7656 (p) REVERT: A 207 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7093 (mmtp) REVERT: A 239 ARG cc_start: 0.5766 (mtt180) cc_final: 0.5262 (mtm-85) REVERT: A 242 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.5957 (mp0) REVERT: A 253 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6136 (mptt) REVERT: A 302 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6650 (m-30) REVERT: A 340 LYS cc_start: 0.6997 (tptp) cc_final: 0.6526 (ttpt) REVERT: A 406 LYS cc_start: 0.6937 (pttp) cc_final: 0.6576 (ptpt) REVERT: B 21 LYS cc_start: 0.8071 (mtmt) cc_final: 0.7454 (mtmm) REVERT: B 68 LYS cc_start: 0.6660 (mtmt) cc_final: 0.6284 (mtmt) REVERT: B 73 ASN cc_start: 0.7604 (m-40) cc_final: 0.7157 (t0) REVERT: B 75 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6736 (pt) REVERT: B 96 ILE cc_start: 0.7848 (mm) cc_final: 0.7484 (pt) REVERT: B 228 LYS cc_start: 0.6618 (ttpt) cc_final: 0.5888 (ttpp) REVERT: B 295 ARG cc_start: 0.6667 (mtp180) cc_final: 0.5531 (mpt-90) REVERT: B 300 SER cc_start: 0.8036 (t) cc_final: 0.7812 (t) REVERT: B 364 ASN cc_start: 0.7318 (m-40) cc_final: 0.6727 (t0) REVERT: C 22 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7324 (mp10) REVERT: C 83 GLU cc_start: 0.7022 (tt0) cc_final: 0.6225 (mp0) REVERT: C 91 LYS cc_start: 0.7496 (ttpt) cc_final: 0.6155 (tttt) REVERT: C 242 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7709 (ttm-80) REVERT: C 251 GLN cc_start: 0.7349 (mt0) cc_final: 0.6938 (mp10) REVERT: C 359 ASN cc_start: 0.6759 (m110) cc_final: 0.6031 (t0) REVERT: D 13 GLU cc_start: 0.6605 (mm-30) cc_final: 0.6196 (mt-10) REVERT: D 47 LYS cc_start: 0.7651 (mtmm) cc_final: 0.7119 (mttp) REVERT: D 73 GLN cc_start: 0.7236 (tt0) cc_final: 0.7020 (mt0) REVERT: D 84 MET cc_start: 0.7268 (mpp) cc_final: 0.7057 (tmm) REVERT: D 172 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6653 (mt-10) REVERT: D 221 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6856 (m-30) REVERT: D 255 ARG cc_start: 0.5952 (mtm110) cc_final: 0.5374 (mtt90) REVERT: D 269 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6530 (mp) REVERT: D 287 ARG cc_start: 0.6107 (OUTLIER) cc_final: 0.5431 (mtp180) REVERT: E 61 GLU cc_start: 0.7077 (tt0) cc_final: 0.6733 (mt-10) REVERT: E 94 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7109 (mtp180) REVERT: E 98 SER cc_start: 0.6900 (t) cc_final: 0.6509 (m) REVERT: F 23 GLU cc_start: 0.7538 (tt0) cc_final: 0.7186 (tt0) REVERT: F 58 GLN cc_start: 0.7383 (mp-120) cc_final: 0.6075 (tp-100) REVERT: F 81 GLU cc_start: 0.6837 (mp0) cc_final: 0.5856 (mm-30) REVERT: F 97 ARG cc_start: 0.7315 (mmm160) cc_final: 0.6872 (mmm160) REVERT: F 107 LYS cc_start: 0.7079 (mmmm) cc_final: 0.6681 (mttt) REVERT: F 110 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7403 (tm130) REVERT: F 119 THR cc_start: 0.7338 (m) cc_final: 0.7048 (p) REVERT: F 145 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.5349 (mm-30) REVERT: G 135 GLU cc_start: 0.6669 (tt0) cc_final: 0.6421 (tt0) REVERT: H 28 ARG cc_start: 0.7705 (tpp-160) cc_final: 0.7401 (tpp80) REVERT: H 30 VAL cc_start: 0.8708 (m) cc_final: 0.8413 (t) REVERT: H 68 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7430 (mttm) REVERT: H 72 GLU cc_start: 0.7033 (tt0) cc_final: 0.6558 (mp0) REVERT: H 141 SER cc_start: 0.7805 (t) cc_final: 0.7418 (m) REVERT: H 206 ARG cc_start: 0.6495 (ttm-80) cc_final: 0.5316 (ttm110) REVERT: H 234 SER cc_start: 0.7265 (m) cc_final: 0.6941 (t) REVERT: H 306 TYR cc_start: 0.8819 (m-80) cc_final: 0.8480 (m-80) REVERT: H 328 LYS cc_start: 0.6970 (mmmm) cc_final: 0.6715 (mppt) REVERT: I 50 LYS cc_start: 0.7238 (mmpt) cc_final: 0.6788 (mtpm) REVERT: I 68 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7496 (mttt) REVERT: I 152 VAL cc_start: 0.7200 (OUTLIER) cc_final: 0.6983 (p) REVERT: I 180 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7096 (tt) REVERT: I 215 LYS cc_start: 0.7681 (mtpp) cc_final: 0.7290 (mttp) REVERT: I 305 MET cc_start: 0.8363 (mmm) cc_final: 0.7920 (mmm) REVERT: I 355 MET cc_start: 0.6700 (OUTLIER) cc_final: 0.6376 (mtt) REVERT: M 66 THR cc_start: 0.7684 (m) cc_final: 0.7389 (p) REVERT: M 78 ASN cc_start: 0.7572 (t0) cc_final: 0.7115 (t0) REVERT: M 194 THR cc_start: 0.8181 (m) cc_final: 0.7910 (p) REVERT: M 202 THR cc_start: 0.7216 (m) cc_final: 0.6861 (p) REVERT: N 47 MET cc_start: 0.0964 (ttp) cc_final: 0.0303 (ttm) REVERT: N 206 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6513 (ttm110) REVERT: N 211 ASP cc_start: 0.7605 (m-30) cc_final: 0.7340 (t70) REVERT: N 305 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7822 (mmt) REVERT: N 328 LYS cc_start: 0.7492 (tptt) cc_final: 0.7056 (tptm) REVERT: O 68 LYS cc_start: 0.7959 (ptmt) cc_final: 0.7434 (mtpp) REVERT: O 100 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7779 (mt-10) REVERT: O 176 MET cc_start: 0.8504 (mmm) cc_final: 0.8284 (mmm) REVERT: O 206 ARG cc_start: 0.7432 (ttp-170) cc_final: 0.6239 (ttm-80) REVERT: O 276 GLU cc_start: 0.7093 (tt0) cc_final: 0.6803 (tt0) REVERT: O 284 LYS cc_start: 0.8052 (mttm) cc_final: 0.7630 (mttm) REVERT: O 286 ASP cc_start: 0.6844 (t0) cc_final: 0.6530 (m-30) REVERT: O 326 LYS cc_start: 0.7577 (ptpp) cc_final: 0.6819 (mmmt) REVERT: O 328 LYS cc_start: 0.7694 (mtmt) cc_final: 0.6951 (mttp) REVERT: O 336 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7467 (tptp) REVERT: O 359 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7659 (tptp) REVERT: P 82 MET cc_start: 0.7893 (tpt) cc_final: 0.7273 (tpt) REVERT: P 206 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6321 (ttm110) REVERT: P 355 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7938 (mpp) REVERT: P 359 LYS cc_start: 0.7270 (ptmm) cc_final: 0.6854 (tptt) REVERT: Q 34 ILE cc_start: 0.8398 (mt) cc_final: 0.8041 (pt) REVERT: Q 47 MET cc_start: 0.6851 (mmm) cc_final: 0.5651 (ptt) REVERT: Q 60 SER cc_start: 0.7719 (t) cc_final: 0.7399 (p) REVERT: Q 61 LYS cc_start: 0.7578 (mtpp) cc_final: 0.7149 (mtpp) REVERT: Q 72 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6964 (mt-10) REVERT: Q 190 MET cc_start: 0.7364 (mtm) cc_final: 0.7110 (mtp) REVERT: Q 286 ASP cc_start: 0.7919 (m-30) cc_final: 0.7699 (m-30) REVERT: Q 291 LYS cc_start: 0.5384 (mttm) cc_final: 0.4757 (tmtm) REVERT: Q 313 MET cc_start: 0.7973 (tpt) cc_final: 0.7653 (mmm) REVERT: Q 314 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: Q 328 LYS cc_start: 0.7318 (ttmt) cc_final: 0.6555 (ttmt) REVERT: Q 336 LYS cc_start: 0.7777 (tptm) cc_final: 0.7432 (ttmt) REVERT: Q 354 GLN cc_start: 0.7598 (pm20) cc_final: 0.7250 (mm110) REVERT: R 37 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.5796 (mpp-170) REVERT: R 72 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7328 (mt-10) REVERT: R 99 GLU cc_start: 0.7415 (pt0) cc_final: 0.7147 (pm20) REVERT: R 206 ARG cc_start: 0.6772 (tpp80) cc_final: 0.6179 (ttm-80) REVERT: R 215 LYS cc_start: 0.7568 (mmmt) cc_final: 0.7230 (mmtm) REVERT: R 225 ASN cc_start: 0.6573 (t0) cc_final: 0.6134 (m-40) REVERT: R 358 THR cc_start: 0.7622 (m) cc_final: 0.7296 (p) outliers start: 107 outliers final: 60 residues processed: 650 average time/residue: 2.8714 time to fit residues: 2263.5461 Evaluate side-chains 646 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 561 time to evaluate : 4.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 336 LYS Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 336 LYS Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 314 GLN Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 247 VAL 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 288 optimal weight: 2.9990 chunk 464 optimal weight: 5.9990 chunk 283 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 322 optimal weight: 3.9990 chunk 487 optimal weight: 0.6980 chunk 448 optimal weight: 2.9990 chunk 387 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 299 optimal weight: 0.7980 chunk 237 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 ASN G 19 GLN ** I 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 297 ASN O 225 ASN R 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39895 Z= 0.197 Angle : 0.562 6.981 54139 Z= 0.277 Chirality : 0.043 0.174 5990 Planarity : 0.004 0.089 6962 Dihedral : 8.237 165.371 5545 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.14 % Allowed : 17.01 % Favored : 80.85 % 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: 0.35 (0.12), residues: 4854 helix: 0.35 (0.12), residues: 1984 sheet: -0.19 (0.17), residues: 856 loop : 0.57 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 356 HIS 0.009 0.001 HIS I 173 PHE 0.016 0.001 PHE D 10 TYR 0.025 0.001 TYR A 402 ARG 0.011 0.000 ARG F 42 ********************** 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 657 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 567 time to evaluate : 4.779 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: A 100 GLU cc_start: 0.7361 (pt0) cc_final: 0.7051 (pp20) REVERT: A 137 GLU cc_start: 0.6186 (OUTLIER) cc_final: 0.5956 (mp0) REVERT: A 204 SER cc_start: 0.7869 (OUTLIER) cc_final: 0.7661 (p) REVERT: A 207 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7132 (mmtp) REVERT: A 239 ARG cc_start: 0.5753 (mtt180) cc_final: 0.5252 (mtm-85) REVERT: A 242 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.5937 (mp0) REVERT: A 253 LYS cc_start: 0.6547 (OUTLIER) cc_final: 0.6136 (mptt) REVERT: A 302 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6672 (m-30) REVERT: A 340 LYS cc_start: 0.6988 (tptp) cc_final: 0.6573 (ttpt) REVERT: A 406 LYS cc_start: 0.6917 (pttp) cc_final: 0.6561 (ptpt) REVERT: B 21 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7461 (mtmm) REVERT: B 68 LYS cc_start: 0.6658 (mtmt) cc_final: 0.6283 (mtmt) REVERT: B 73 ASN cc_start: 0.7586 (m-40) cc_final: 0.7142 (t0) REVERT: B 75 ILE cc_start: 0.7022 (OUTLIER) cc_final: 0.6751 (pt) REVERT: B 96 ILE cc_start: 0.7789 (mm) cc_final: 0.7461 (pt) REVERT: B 228 LYS cc_start: 0.6614 (ttpt) cc_final: 0.5883 (ttpp) REVERT: B 295 ARG cc_start: 0.6667 (mtp180) cc_final: 0.5527 (mpt-90) REVERT: B 300 SER cc_start: 0.8019 (t) cc_final: 0.7795 (t) REVERT: B 364 ASN cc_start: 0.7304 (m-40) cc_final: 0.6700 (t0) REVERT: C 22 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7327 (mp10) REVERT: C 83 GLU cc_start: 0.7014 (tt0) cc_final: 0.6219 (mp0) REVERT: C 91 LYS cc_start: 0.7501 (ttpt) cc_final: 0.6131 (tttt) REVERT: C 242 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7698 (ttm-80) REVERT: C 251 GLN cc_start: 0.7344 (mt0) cc_final: 0.6934 (mp10) REVERT: C 359 ASN cc_start: 0.6764 (m110) cc_final: 0.6038 (t0) REVERT: D 13 GLU cc_start: 0.6556 (mm-30) cc_final: 0.6147 (mt-10) REVERT: D 47 LYS cc_start: 0.7620 (mtmm) cc_final: 0.7082 (mttp) REVERT: D 73 GLN cc_start: 0.7184 (tt0) cc_final: 0.6961 (mt0) REVERT: D 84 MET cc_start: 0.7271 (mpp) cc_final: 0.7053 (tmm) REVERT: D 172 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6676 (mt-10) REVERT: D 255 ARG cc_start: 0.5958 (mtm110) cc_final: 0.5375 (mtt90) REVERT: D 269 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6499 (mp) REVERT: D 287 ARG cc_start: 0.6020 (OUTLIER) cc_final: 0.5363 (mtp180) REVERT: E 61 GLU cc_start: 0.7072 (tt0) cc_final: 0.6716 (mt-10) REVERT: E 94 ARG cc_start: 0.7613 (mtp180) cc_final: 0.7138 (mtp180) REVERT: E 98 SER cc_start: 0.6895 (t) cc_final: 0.6509 (m) REVERT: F 23 GLU cc_start: 0.7550 (tt0) cc_final: 0.7190 (tt0) REVERT: F 58 GLN cc_start: 0.7406 (mp-120) cc_final: 0.6102 (tp-100) REVERT: F 81 GLU cc_start: 0.6816 (mp0) cc_final: 0.5813 (mm-30) REVERT: F 97 ARG cc_start: 0.7298 (mmm160) cc_final: 0.6856 (mmm160) REVERT: F 107 LYS cc_start: 0.7088 (mmmm) cc_final: 0.6679 (mttt) REVERT: F 110 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7373 (tm130) REVERT: F 119 THR cc_start: 0.7320 (m) cc_final: 0.7029 (p) REVERT: F 145 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.5300 (mm-30) REVERT: G 135 GLU cc_start: 0.6655 (tt0) cc_final: 0.6411 (tt0) REVERT: H 28 ARG cc_start: 0.7707 (tpp-160) cc_final: 0.7404 (tpp80) REVERT: H 30 VAL cc_start: 0.8723 (m) cc_final: 0.8446 (t) REVERT: H 68 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7413 (mttm) REVERT: H 72 GLU cc_start: 0.7033 (tt0) cc_final: 0.6554 (mp0) REVERT: H 141 SER cc_start: 0.7790 (t) cc_final: 0.7401 (m) REVERT: H 206 ARG cc_start: 0.6534 (ttm-80) cc_final: 0.5394 (ttm110) REVERT: H 234 SER cc_start: 0.7237 (m) cc_final: 0.6923 (t) REVERT: H 306 TYR cc_start: 0.8807 (m-80) cc_final: 0.8470 (m-80) REVERT: H 328 LYS cc_start: 0.6975 (mmmm) cc_final: 0.6721 (mppt) REVERT: I 50 LYS cc_start: 0.7222 (mmpt) cc_final: 0.6809 (mtpt) REVERT: I 68 LYS cc_start: 0.8079 (mmmt) cc_final: 0.7518 (mttt) REVERT: I 152 VAL cc_start: 0.7194 (OUTLIER) cc_final: 0.6976 (p) REVERT: I 180 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7098 (tt) REVERT: I 215 LYS cc_start: 0.7678 (mtpp) cc_final: 0.7289 (mttp) REVERT: I 305 MET cc_start: 0.8354 (mmm) cc_final: 0.8084 (mmm) REVERT: I 355 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.6309 (mtt) REVERT: M 66 THR cc_start: 0.7716 (m) cc_final: 0.7432 (p) REVERT: M 78 ASN cc_start: 0.7561 (t0) cc_final: 0.7145 (t0) REVERT: M 83 GLU cc_start: 0.7133 (tt0) cc_final: 0.6487 (tm-30) REVERT: M 194 THR cc_start: 0.8179 (m) cc_final: 0.7917 (p) REVERT: M 202 THR cc_start: 0.7171 (m) cc_final: 0.6819 (p) REVERT: N 47 MET cc_start: 0.0930 (ttp) cc_final: 0.0272 (ttm) REVERT: N 206 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6523 (ttm110) REVERT: N 211 ASP cc_start: 0.7571 (m-30) cc_final: 0.7310 (t70) REVERT: N 236 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7592 (mp) REVERT: N 305 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7815 (mmt) REVERT: N 328 LYS cc_start: 0.7410 (tptt) cc_final: 0.7007 (tptm) REVERT: O 68 LYS cc_start: 0.7953 (ptmt) cc_final: 0.7436 (mtpp) REVERT: O 100 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7796 (mt-10) REVERT: O 206 ARG cc_start: 0.7416 (ttp-170) cc_final: 0.6219 (ttm-80) REVERT: O 276 GLU cc_start: 0.7064 (tt0) cc_final: 0.6808 (tt0) REVERT: O 284 LYS cc_start: 0.8060 (mttm) cc_final: 0.7644 (mttm) REVERT: O 286 ASP cc_start: 0.6820 (t0) cc_final: 0.6523 (m-30) REVERT: O 326 LYS cc_start: 0.7559 (ptpp) cc_final: 0.6784 (mmmt) REVERT: O 328 LYS cc_start: 0.7695 (mtmt) cc_final: 0.6959 (mttp) REVERT: O 336 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7470 (tptp) REVERT: O 359 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7653 (tptp) REVERT: P 82 MET cc_start: 0.7914 (tpt) cc_final: 0.7312 (tpt) REVERT: P 206 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6319 (ttm110) REVERT: P 355 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7954 (mpp) REVERT: P 359 LYS cc_start: 0.7265 (ptmm) cc_final: 0.6858 (tptt) REVERT: Q 34 ILE cc_start: 0.8410 (mt) cc_final: 0.8068 (pt) REVERT: Q 47 MET cc_start: 0.6828 (mmm) cc_final: 0.5681 (ptt) REVERT: Q 57 GLU cc_start: 0.7542 (tt0) cc_final: 0.7283 (tt0) REVERT: Q 60 SER cc_start: 0.7698 (t) cc_final: 0.7383 (p) REVERT: Q 61 LYS cc_start: 0.7561 (mtpp) cc_final: 0.7132 (mtpp) REVERT: Q 72 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6955 (mt-10) REVERT: Q 190 MET cc_start: 0.7346 (mtm) cc_final: 0.7093 (mtp) REVERT: Q 286 ASP cc_start: 0.7881 (m-30) cc_final: 0.7675 (m-30) REVERT: Q 291 LYS cc_start: 0.5373 (mttm) cc_final: 0.4765 (tmtm) REVERT: Q 313 MET cc_start: 0.7951 (tpt) cc_final: 0.7629 (mmm) REVERT: Q 314 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: Q 328 LYS cc_start: 0.7305 (ttmt) cc_final: 0.6542 (ttmt) REVERT: Q 336 LYS cc_start: 0.7769 (tptm) cc_final: 0.7435 (ttmt) REVERT: R 37 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.5786 (mpp-170) REVERT: R 72 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7354 (mt-10) REVERT: R 99 GLU cc_start: 0.7404 (pt0) cc_final: 0.7142 (pm20) REVERT: R 206 ARG cc_start: 0.6774 (tpp80) cc_final: 0.6182 (ttm-80) REVERT: R 215 LYS cc_start: 0.7567 (mmmt) cc_final: 0.7226 (mmtm) REVERT: R 225 ASN cc_start: 0.6561 (t0) cc_final: 0.6124 (m-40) REVERT: R 358 THR cc_start: 0.7608 (m) cc_final: 0.7293 (p) outliers start: 90 outliers final: 56 residues processed: 632 average time/residue: 2.9366 time to fit residues: 2250.0218 Evaluate side-chains 638 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 557 time to evaluate : 4.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 336 LYS Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 314 GLN Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain R residue 247 VAL 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: 9.9990 chunk 413 optimal weight: 0.4980 chunk 118 optimal weight: 4.9990 chunk 357 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 388 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 398 optimal weight: 1.9990 chunk 49 optimal weight: 0.0470 chunk 71 optimal weight: 1.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 143 ASN ** I 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 ASN O 225 ASN R 137 GLN R 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.114843 restraints weight = 133444.841| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.44 r_work: 0.3316 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 39895 Z= 0.157 Angle : 0.539 7.503 54139 Z= 0.263 Chirality : 0.042 0.146 5990 Planarity : 0.004 0.093 6962 Dihedral : 7.799 170.828 5545 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.62 % Allowed : 17.68 % Favored : 80.71 % 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: 0.53 (0.12), residues: 4854 helix: 0.52 (0.12), residues: 1991 sheet: -0.14 (0.17), residues: 861 loop : 0.68 (0.15), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 356 HIS 0.008 0.001 HIS I 173 PHE 0.012 0.001 PHE D 10 TYR 0.014 0.001 TYR I 279 ARG 0.013 0.000 ARG F 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32774.65 seconds wall clock time: 562 minutes 21.38 seconds (33741.38 seconds total)