Starting phenix.real_space_refine on Mon Mar 25 15:10:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm7_4590/03_2024/6qm7_4590_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm7_4590/03_2024/6qm7_4590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm7_4590/03_2024/6qm7_4590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm7_4590/03_2024/6qm7_4590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm7_4590/03_2024/6qm7_4590_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm7_4590/03_2024/6qm7_4590_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians S 328 5.16 5 C 30912 2.51 5 N 8480 2.21 5 O 9796 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ASP 61": "OD1" <-> "OD2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 146": "OD1" <-> "OD2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C GLU 123": "OE1" <-> "OE2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ASP 161": "OD1" <-> "OD2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C ASP 214": "OD1" <-> "OD2" Residue "C GLU 217": "OE1" <-> "OE2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D ASP 105": "OD1" <-> "OD2" Residue "D TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 215": "NH1" <-> "NH2" Residue "D TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 141": "NH1" <-> "NH2" Residue "E GLU 151": "OE1" <-> "OE2" Residue "E GLU 195": "OE1" <-> "OE2" Residue "E GLU 248": "OE1" <-> "OE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E ARG 284": "NH1" <-> "NH2" Residue "E TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 287": "NH1" <-> "NH2" Residue "E GLU 292": "OE1" <-> "OE2" Residue "E GLU 295": "OE1" <-> "OE2" Residue "E GLU 313": "OE1" <-> "OE2" Residue "E ASP 323": "OD1" <-> "OD2" Residue "E ASP 324": "OD1" <-> "OD2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 232": "OD1" <-> "OD2" Residue "F GLU 233": "OE1" <-> "OE2" Residue "F ARG 251": "NH1" <-> "NH2" Residue "F TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 279": "OE1" <-> "OE2" Residue "F ASP 317": "OD1" <-> "OD2" Residue "F ASP 320": "OD1" <-> "OD2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 346": "OD1" <-> "OD2" Residue "F ASP 383": "OD1" <-> "OD2" Residue "F PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 391": "OE1" <-> "OE2" Residue "F GLU 392": "OE1" <-> "OE2" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 9": "OD1" <-> "OD2" Residue "G ASP 13": "OD1" <-> "OD2" Residue "G GLU 18": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ARG 66": "NH1" <-> "NH2" Residue "G ARG 86": "NH1" <-> "NH2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "G ARG 115": "NH1" <-> "NH2" Residue "G TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 130": "NH1" <-> "NH2" Residue "G PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 143": "OD1" <-> "OD2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 175": "OE1" <-> "OE2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "G ASP 202": "OD1" <-> "OD2" Residue "G TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 210": "OE1" <-> "OE2" Residue "G ASP 221": "OD1" <-> "OD2" Residue "G PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 230": "OD1" <-> "OD2" Residue "H TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 99": "NH1" <-> "NH2" Residue "H ARG 112": "NH1" <-> "NH2" Residue "H TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 194": "OD1" <-> "OD2" Residue "H GLU 237": "OE1" <-> "OE2" Residue "H ARG 247": "NH1" <-> "NH2" Residue "H TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 255": "OD1" <-> "OD2" Residue "H PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 278": "NH1" <-> "NH2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "I TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "I PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 189": "NH1" <-> "NH2" Residue "I ASP 219": "OD1" <-> "OD2" Residue "I GLU 223": "OE1" <-> "OE2" Residue "I ARG 224": "NH1" <-> "NH2" Residue "J GLU 18": "OE1" <-> "OE2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 30": "OE1" <-> "OE2" Residue "J GLU 38": "OE1" <-> "OE2" Residue "J TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 59": "OD1" <-> "OD2" Residue "J PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 72": "OE1" <-> "OE2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 77": "NH1" <-> "NH2" Residue "J GLU 78": "OE1" <-> "OE2" Residue "J ASP 81": "OD1" <-> "OD2" Residue "J GLU 97": "OE1" <-> "OE2" Residue "J GLU 118": "OE1" <-> "OE2" Residue "J GLU 132": "OE1" <-> "OE2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "J GLU 144": "OE1" <-> "OE2" Residue "J GLU 151": "OE1" <-> "OE2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "J GLU 165": "OE1" <-> "OE2" Residue "J TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 203": "NH1" <-> "NH2" Residue "K TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 33": "OE1" <-> "OE2" Residue "K GLU 50": "OE1" <-> "OE2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 111": "OD1" <-> "OD2" Residue "K TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 130": "OD1" <-> "OD2" Residue "K TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "K ASP 176": "OD1" <-> "OD2" Residue "K ARG 181": "NH1" <-> "NH2" Residue "K TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 200": "OE1" <-> "OE2" Residue "L ARG 106": "NH1" <-> "NH2" Residue "L PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L ARG 168": "NH1" <-> "NH2" Residue "L ARG 172": "NH1" <-> "NH2" Residue "L TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 190": "NH1" <-> "NH2" Residue "L ASP 204": "OD1" <-> "OD2" Residue "L TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 131": "OD1" <-> "OD2" Residue "M PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "M ASP 164": "OD1" <-> "OD2" Residue "M TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 241": "OE1" <-> "OE2" Residue "M GLU 242": "OE1" <-> "OE2" Residue "M TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 264": "NH1" <-> "NH2" Residue "M PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 335": "OE1" <-> "OE2" Residue "M ARG 337": "NH1" <-> "NH2" Residue "M ASP 339": "OD1" <-> "OD2" Residue "N TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 55": "OD1" <-> "OD2" Residue "N ASP 65": "OD1" <-> "OD2" Residue "N GLU 68": "OE1" <-> "OE2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ASP 77": "OD1" <-> "OD2" Residue "N ARG 90": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ASP 98": "OD1" <-> "OD2" Residue "N PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 100": "OD1" <-> "OD2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 112": "NH1" <-> "NH2" Residue "N ASP 113": "OD1" <-> "OD2" Residue "N ASP 123": "OD1" <-> "OD2" Residue "N GLU 129": "OE1" <-> "OE2" Residue "N GLU 161": "OE1" <-> "OE2" Residue "N ASP 168": "OD1" <-> "OD2" Residue "N ARG 171": "NH1" <-> "NH2" Residue "N ARG 179": "NH1" <-> "NH2" Residue "N ASP 188": "OD1" <-> "OD2" Residue "N ASP 192": "OD1" <-> "OD2" Residue "N PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 40": "NH1" <-> "NH2" Residue "O ARG 56": "NH1" <-> "NH2" Residue "O ASP 61": "OD1" <-> "OD2" Residue "O TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 90": "NH1" <-> "NH2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 146": "OD1" <-> "OD2" Residue "O ASP 157": "OD1" <-> "OD2" Residue "O PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 182": "OE1" <-> "OE2" Residue "O GLU 240": "OE1" <-> "OE2" Residue "P GLU 3": "OE1" <-> "OE2" Residue "P GLU 21": "OE1" <-> "OE2" Residue "P PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 68": "OE1" <-> "OE2" Residue "P TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 101": "OE1" <-> "OE2" Residue "P PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 167": "OD1" <-> "OD2" Residue "P GLU 173": "OE1" <-> "OE2" Residue "P ARG 175": "NH1" <-> "NH2" Residue "P GLU 183": "OE1" <-> "OE2" Residue "P PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 198": "OD1" <-> "OD2" Residue "P ARG 215": "NH1" <-> "NH2" Residue "P PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 217": "OE1" <-> "OE2" Residue "P ARG 225": "NH1" <-> "NH2" Residue "P ASP 226": "OD1" <-> "OD2" Residue "Q ARG 4": "NH1" <-> "NH2" Residue "Q GLU 59": "OE1" <-> "OE2" Residue "Q ASP 63": "OD1" <-> "OD2" Residue "Q GLU 76": "OE1" <-> "OE2" Residue "Q GLU 109": "OE1" <-> "OE2" Residue "Q GLU 114": "OE1" <-> "OE2" Residue "Q ARG 118": "NH1" <-> "NH2" Residue "Q GLU 123": "OE1" <-> "OE2" Residue "Q TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 147": "NH1" <-> "NH2" Residue "Q ASP 161": "OD1" <-> "OD2" Residue "Q TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 184": "OD1" <-> "OD2" Residue "Q ASP 214": "OD1" <-> "OD2" Residue "Q GLU 217": "OE1" <-> "OE2" Residue "Q ARG 222": "NH1" <-> "NH2" Residue "Q ARG 265": "NH1" <-> "NH2" Residue "R ASP 55": "OD1" <-> "OD2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 99": "OE1" <-> "OE2" Residue "R ASP 105": "OD1" <-> "OD2" Residue "R TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 139": "OD1" <-> "OD2" Residue "R ASP 148": "OD1" <-> "OD2" Residue "R ARG 157": "NH1" <-> "NH2" Residue "R ARG 182": "NH1" <-> "NH2" Residue "R PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 195": "OE1" <-> "OE2" Residue "R ARG 202": "NH1" <-> "NH2" Residue "R ARG 215": "NH1" <-> "NH2" Residue "R TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 230": "OE1" <-> "OE2" Residue "R GLU 232": "OE1" <-> "OE2" Residue "R GLU 234": "OE1" <-> "OE2" Residue "R GLU 235": "OE1" <-> "OE2" Residue "R GLU 236": "OE1" <-> "OE2" Residue "S GLU 107": "OE1" <-> "OE2" Residue "S PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 120": "NH1" <-> "NH2" Residue "S ARG 141": "NH1" <-> "NH2" Residue "S GLU 151": "OE1" <-> "OE2" Residue "S GLU 195": "OE1" <-> "OE2" Residue "S GLU 248": "OE1" <-> "OE2" Residue "S ARG 284": "NH1" <-> "NH2" Residue "S TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 287": "NH1" <-> "NH2" Residue "S GLU 292": "OE1" <-> "OE2" Residue "S GLU 295": "OE1" <-> "OE2" Residue "S GLU 313": "OE1" <-> "OE2" Residue "S ASP 323": "OD1" <-> "OD2" Residue "S ASP 324": "OD1" <-> "OD2" Residue "T GLU 169": "OE1" <-> "OE2" Residue "T GLU 187": "OE1" <-> "OE2" Residue "T GLU 191": "OE1" <-> "OE2" Residue "T PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 232": "OD1" <-> "OD2" Residue "T GLU 233": "OE1" <-> "OE2" Residue "T ARG 251": "NH1" <-> "NH2" Residue "T TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 279": "OE1" <-> "OE2" Residue "T ASP 317": "OD1" <-> "OD2" Residue "T ASP 320": "OD1" <-> "OD2" Residue "T GLU 338": "OE1" <-> "OE2" Residue "T ARG 339": "NH1" <-> "NH2" Residue "T PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 346": "OD1" <-> "OD2" Residue "T ASP 383": "OD1" <-> "OD2" Residue "T GLU 391": "OE1" <-> "OE2" Residue "T GLU 392": "OE1" <-> "OE2" Residue "T PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 9": "OD1" <-> "OD2" Residue "U ASP 13": "OD1" <-> "OD2" Residue "U GLU 18": "OE1" <-> "OE2" Residue "U GLU 60": "OE1" <-> "OE2" Residue "U ARG 66": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 91": "NH1" <-> "NH2" Residue "U GLU 97": "OE1" <-> "OE2" Residue "U ARG 100": "NH1" <-> "NH2" Residue "U ARG 115": "NH1" <-> "NH2" Residue "U TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 130": "NH1" <-> "NH2" Residue "U PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 143": "OD1" <-> "OD2" Residue "U ASP 152": "OD1" <-> "OD2" Residue "U TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 175": "OE1" <-> "OE2" Residue "U ASP 187": "OD1" <-> "OD2" Residue "U GLU 199": "OE1" <-> "OE2" Residue "U ASP 202": "OD1" <-> "OD2" Residue "U TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 210": "OE1" <-> "OE2" Residue "U ASP 221": "OD1" <-> "OD2" Residue "U PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 230": "OD1" <-> "OD2" Residue "V TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 99": "NH1" <-> "NH2" Residue "V ARG 112": "NH1" <-> "NH2" Residue "V TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 194": "OD1" <-> "OD2" Residue "V GLU 237": "OE1" <-> "OE2" Residue "V ARG 247": "NH1" <-> "NH2" Residue "V TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 255": "OD1" <-> "OD2" Residue "V PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 278": "NH1" <-> "NH2" Residue "W TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 61": "NH1" <-> "NH2" Residue "W TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 104": "NH1" <-> "NH2" Residue "W PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 189": "NH1" <-> "NH2" Residue "W ASP 219": "OD1" <-> "OD2" Residue "W GLU 223": "OE1" <-> "OE2" Residue "W ARG 224": "NH1" <-> "NH2" Residue "X GLU 18": "OE1" <-> "OE2" Residue "X PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 30": "OE1" <-> "OE2" Residue "X GLU 38": "OE1" <-> "OE2" Residue "X TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 59": "OD1" <-> "OD2" Residue "X PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 72": "OE1" <-> "OE2" Residue "X TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X GLU 78": "OE1" <-> "OE2" Residue "X ASP 81": "OD1" <-> "OD2" Residue "X GLU 97": "OE1" <-> "OE2" Residue "X GLU 118": "OE1" <-> "OE2" Residue "X GLU 132": "OE1" <-> "OE2" Residue "X GLU 134": "OE1" <-> "OE2" Residue "X GLU 144": "OE1" <-> "OE2" Residue "X GLU 151": "OE1" <-> "OE2" Residue "X GLU 161": "OE1" <-> "OE2" Residue "X GLU 165": "OE1" <-> "OE2" Residue "X ARG 203": "NH1" <-> "NH2" Residue "Y TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 33": "OE1" <-> "OE2" Residue "Y GLU 50": "OE1" <-> "OE2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 69": "NH1" <-> "NH2" Residue "Y GLU 80": "OE1" <-> "OE2" Residue "Y TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 111": "OD1" <-> "OD2" Residue "Y TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 130": "OD1" <-> "OD2" Residue "Y TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 166": "OE1" <-> "OE2" Residue "Y ASP 176": "OD1" <-> "OD2" Residue "Y ARG 181": "NH1" <-> "NH2" Residue "Y TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 200": "OE1" <-> "OE2" Residue "Z ARG 106": "NH1" <-> "NH2" Residue "Z PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 155": "OE1" <-> "OE2" Residue "Z ARG 168": "NH1" <-> "NH2" Residue "Z ARG 172": "NH1" <-> "NH2" Residue "Z TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 190": "NH1" <-> "NH2" Residue "Z ASP 204": "OD1" <-> "OD2" Residue "Z TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 131": "OD1" <-> "OD2" Residue "a PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a ASP 164": "OD1" <-> "OD2" Residue "a TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 241": "OE1" <-> "OE2" Residue "a GLU 242": "OE1" <-> "OE2" Residue "a TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 264": "NH1" <-> "NH2" Residue "a PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 335": "OE1" <-> "OE2" Residue "a ARG 337": "NH1" <-> "NH2" Residue "a ASP 339": "OD1" <-> "OD2" Residue "b TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 55": "OD1" <-> "OD2" Residue "b ASP 65": "OD1" <-> "OD2" Residue "b GLU 68": "OE1" <-> "OE2" Residue "b ARG 69": "NH1" <-> "NH2" Residue "b ASP 77": "OD1" <-> "OD2" Residue "b ARG 90": "NH1" <-> "NH2" Residue "b ARG 96": "NH1" <-> "NH2" Residue "b ASP 98": "OD1" <-> "OD2" Residue "b PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 100": "OD1" <-> "OD2" Residue "b PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 112": "NH1" <-> "NH2" Residue "b ASP 113": "OD1" <-> "OD2" Residue "b ASP 123": "OD1" <-> "OD2" Residue "b GLU 129": "OE1" <-> "OE2" Residue "b GLU 161": "OE1" <-> "OE2" Residue "b ASP 168": "OD1" <-> "OD2" Residue "b ARG 171": "NH1" <-> "NH2" Residue "b ARG 179": "NH1" <-> "NH2" Residue "b ASP 188": "OD1" <-> "OD2" Residue "b ASP 192": "OD1" <-> "OD2" Residue "b PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 203": "OE1" <-> "OE2" Residue "b TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49518 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1857 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "B" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "C" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2195 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "D" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1873 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 4, 'TRANS': 234} Chain: "E" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1756 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "F" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "G" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1727 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1710 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "I" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "J" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "K" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "L" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1579 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 2, 'TRANS': 199} Chain: "M" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "N" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "O" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1857 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "P" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "Q" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2195 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "R" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1873 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 4, 'TRANS': 234} Chain: "S" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1756 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "T" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "U" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1727 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "V" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1710 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "W" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "X" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "Y" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "Z" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1579 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 2, 'TRANS': 199} Chain: "a" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "b" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'J6E': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'J6E': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "I" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "K" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "M" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "N" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "O" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "P" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "Q" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "S" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "T" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "U" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "V" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "W" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "X" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "Y" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Z" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "a" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "b" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 24.35, per 1000 atoms: 0.49 Number of scatterers: 49518 At special positions: 0 Unit cell: (151.94, 203.3, 138.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 328 16.00 F 2 9.00 O 9796 8.00 N 8480 7.00 C 30912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.03 Conformation dependent library (CDL) restraints added in 9.3 seconds 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11708 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 158 helices and 68 sheets defined 35.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.19 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.626A pdb=" N LYS A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 81 through 102 Processing helix chain 'A' and resid 108 through 124 removed outlier: 3.609A pdb=" N ARG A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.627A pdb=" N LYS A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 210 Processing helix chain 'A' and resid 236 through 248 Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 78 through 99 removed outlier: 3.639A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 removed outlier: 3.560A pdb=" N ILE B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 175 Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.767A pdb=" N GLY B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 228 removed outlier: 3.552A pdb=" N TYR B 227 " --> pdb=" O GLN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 19 through 28 Processing helix chain 'C' and resid 86 through 107 Processing helix chain 'C' and resid 113 through 128 removed outlier: 3.935A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 184 removed outlier: 3.798A pdb=" N ASP C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 205 Processing helix chain 'C' and resid 251 through 276 Proline residue: C 256 - end of helix removed outlier: 3.638A pdb=" N GLN C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 77 through 97 Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.524A pdb=" N THR D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 175 removed outlier: 3.761A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER D 175 " --> pdb=" O TYR D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.539A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 239 removed outlier: 3.595A pdb=" N LYS D 224 " --> pdb=" O GLU D 220 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 removed outlier: 3.524A pdb=" N ILE E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS E 132 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 133 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 203 removed outlier: 3.720A pdb=" N ILE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 221 removed outlier: 3.774A pdb=" N LEU E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER E 220 " --> pdb=" O THR E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 284 removed outlier: 3.599A pdb=" N SER E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 305 Processing helix chain 'E' and resid 332 through 340 removed outlier: 3.508A pdb=" N ILE E 338 " --> pdb=" O GLU E 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 195 removed outlier: 3.672A pdb=" N VAL F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 264 Processing helix chain 'F' and resid 270 through 285 removed outlier: 3.806A pdb=" N HIS F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 343 removed outlier: 3.642A pdb=" N HIS F 340 " --> pdb=" O TYR F 336 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLU F 342 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N HIS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 362 Processing helix chain 'F' and resid 394 through 398 Processing helix chain 'G' and resid 7 through 9 No H-bonds generated for 'chain 'G' and resid 7 through 9' Processing helix chain 'G' and resid 22 through 32 removed outlier: 3.586A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 103 Processing helix chain 'G' and resid 109 through 124 removed outlier: 3.615A pdb=" N TYR G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 177 Processing helix chain 'G' and resid 186 through 200 removed outlier: 3.858A pdb=" N GLY G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 232 No H-bonds generated for 'chain 'G' and resid 229 through 232' Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'H' and resid 130 through 143 Processing helix chain 'H' and resid 184 through 196 removed outlier: 3.933A pdb=" N ILE H 187 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR H 190 " --> pdb=" O ILE H 187 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER H 191 " --> pdb=" O PHE H 188 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE H 193 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP H 194 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA H 195 " --> pdb=" O PHE H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 220 removed outlier: 3.788A pdb=" N ARG H 220 " --> pdb=" O HIS H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 247 No H-bonds generated for 'chain 'H' and resid 245 through 247' Processing helix chain 'H' and resid 256 through 258 No H-bonds generated for 'chain 'H' and resid 256 through 258' Processing helix chain 'I' and resid 78 through 99 removed outlier: 3.527A pdb=" N LEU I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 118 Processing helix chain 'I' and resid 158 through 170 removed outlier: 4.546A pdb=" N ILE I 161 " --> pdb=" O SER I 158 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA I 162 " --> pdb=" O GLY I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 194 Processing helix chain 'J' and resid 57 through 77 Processing helix chain 'J' and resid 84 through 98 removed outlier: 3.960A pdb=" N ALA J 98 " --> pdb=" O MET J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 153 removed outlier: 3.623A pdb=" N GLY J 148 " --> pdb=" O GLU J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 177 removed outlier: 3.642A pdb=" N ARG J 177 " --> pdb=" O SER J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 71 Processing helix chain 'K' and resid 79 through 95 removed outlier: 3.524A pdb=" N ILE K 94 " --> pdb=" O LEU K 90 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG K 95 " --> pdb=" O ALA K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 157 Processing helix chain 'K' and resid 164 through 181 Processing helix chain 'L' and resid 148 through 168 Processing helix chain 'L' and resid 175 through 188 Processing helix chain 'L' and resid 231 through 241 removed outlier: 4.074A pdb=" N GLY L 236 " --> pdb=" O ILE L 232 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL L 237 " --> pdb=" O TYR L 233 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR L 240 " --> pdb=" O GLY L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 263 Processing helix chain 'L' and resid 291 through 298 removed outlier: 3.500A pdb=" N HIS L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 203 Processing helix chain 'M' and resid 211 through 225 removed outlier: 3.614A pdb=" N ARG M 225 " --> pdb=" O MET M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 268 through 280 Proline residue: M 273 - end of helix Processing helix chain 'M' and resid 294 through 311 Processing helix chain 'N' and resid 53 through 73 Processing helix chain 'N' and resid 81 through 97 Processing helix chain 'N' and resid 136 through 152 removed outlier: 3.658A pdb=" N ILE N 141 " --> pdb=" O GLY N 138 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA N 142 " --> pdb=" O ALA N 139 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU N 143 " --> pdb=" O TYR N 140 " (cutoff:3.500A) Proline residue: N 144 - end of helix removed outlier: 3.679A pdb=" N ARG N 147 " --> pdb=" O PRO N 144 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS N 152 " --> pdb=" O ALA N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 176 Processing helix chain 'N' and resid 209 through 211 No H-bonds generated for 'chain 'N' and resid 209 through 211' Processing helix chain 'N' and resid 213 through 216 No H-bonds generated for 'chain 'N' and resid 213 through 216' Processing helix chain 'O' and resid 20 through 31 removed outlier: 3.651A pdb=" N LYS O 27 " --> pdb=" O GLU O 23 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR O 30 " --> pdb=" O PHE O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 62 No H-bonds generated for 'chain 'O' and resid 60 through 62' Processing helix chain 'O' and resid 81 through 102 Processing helix chain 'O' and resid 108 through 124 removed outlier: 3.575A pdb=" N ARG O 122 " --> pdb=" O LYS O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 187 removed outlier: 3.631A pdb=" N LYS O 186 " --> pdb=" O GLU O 182 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 210 Processing helix chain 'O' and resid 236 through 248 Processing helix chain 'P' and resid 18 through 28 Processing helix chain 'P' and resid 57 through 59 No H-bonds generated for 'chain 'P' and resid 57 through 59' Processing helix chain 'P' and resid 78 through 99 removed outlier: 3.644A pdb=" N VAL P 83 " --> pdb=" O PRO P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 120 removed outlier: 3.590A pdb=" N ILE P 115 " --> pdb=" O LYS P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 175 Processing helix chain 'P' and resid 182 through 196 removed outlier: 3.795A pdb=" N GLY P 196 " --> pdb=" O THR P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 228 removed outlier: 3.558A pdb=" N TYR P 227 " --> pdb=" O GLN P 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 5 No H-bonds generated for 'chain 'Q' and resid 3 through 5' Processing helix chain 'Q' and resid 19 through 28 Processing helix chain 'Q' and resid 86 through 107 Processing helix chain 'Q' and resid 113 through 128 removed outlier: 3.840A pdb=" N TYR Q 127 " --> pdb=" O GLU Q 123 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR Q 128 " --> pdb=" O LYS Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 184 removed outlier: 3.801A pdb=" N ASP Q 184 " --> pdb=" O LEU Q 180 " (cutoff:3.500A) Processing helix chain 'Q' and resid 191 through 205 Processing helix chain 'Q' and resid 251 through 276 Proline residue: Q 256 - end of helix removed outlier: 3.656A pdb=" N GLN Q 276 " --> pdb=" O GLU Q 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 27 Processing helix chain 'R' and resid 77 through 97 Processing helix chain 'R' and resid 104 through 119 removed outlier: 3.504A pdb=" N THR R 119 " --> pdb=" O GLN R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 175 removed outlier: 3.764A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER R 175 " --> pdb=" O TYR R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 195 removed outlier: 3.548A pdb=" N GLU R 195 " --> pdb=" O LYS R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 239 removed outlier: 3.601A pdb=" N LYS R 224 " --> pdb=" O GLU R 220 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE R 225 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU R 232 " --> pdb=" O GLU R 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 133 removed outlier: 3.556A pdb=" N GLU S 129 " --> pdb=" O GLU S 125 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU S 133 " --> pdb=" O GLU S 129 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 203 removed outlier: 3.718A pdb=" N ILE S 187 " --> pdb=" O ALA S 183 " (cutoff:3.500A) Processing helix chain 'S' and resid 209 through 221 removed outlier: 3.783A pdb=" N LEU S 219 " --> pdb=" O ALA S 215 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER S 220 " --> pdb=" O THR S 216 " (cutoff:3.500A) Processing helix chain 'S' and resid 274 through 284 removed outlier: 3.572A pdb=" N SER S 279 " --> pdb=" O GLU S 275 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL S 280 " --> pdb=" O ALA S 276 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU S 283 " --> pdb=" O SER S 279 " (cutoff:3.500A) Processing helix chain 'S' and resid 291 through 305 Processing helix chain 'S' and resid 332 through 341 removed outlier: 3.608A pdb=" N ARG S 341 " --> pdb=" O ALA S 337 " (cutoff:3.500A) Processing helix chain 'T' and resid 184 through 195 removed outlier: 3.674A pdb=" N VAL T 193 " --> pdb=" O ALA T 189 " (cutoff:3.500A) Processing helix chain 'T' and resid 243 through 264 Processing helix chain 'T' and resid 270 through 285 removed outlier: 3.761A pdb=" N HIS T 284 " --> pdb=" O LYS T 280 " (cutoff:3.500A) Processing helix chain 'T' and resid 330 through 343 removed outlier: 3.647A pdb=" N HIS T 340 " --> pdb=" O TYR T 336 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLU T 342 " --> pdb=" O GLU T 338 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N HIS T 343 " --> pdb=" O ARG T 339 " (cutoff:3.500A) Processing helix chain 'T' and resid 349 through 362 Processing helix chain 'T' and resid 394 through 398 Processing helix chain 'U' and resid 7 through 9 No H-bonds generated for 'chain 'U' and resid 7 through 9' Processing helix chain 'U' and resid 22 through 32 removed outlier: 3.587A pdb=" N VAL U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 102 Processing helix chain 'U' and resid 109 through 124 removed outlier: 3.642A pdb=" N TYR U 123 " --> pdb=" O PHE U 119 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR U 124 " --> pdb=" O MET U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 177 Processing helix chain 'U' and resid 186 through 200 removed outlier: 3.838A pdb=" N GLY U 191 " --> pdb=" O ASP U 187 " (cutoff:3.500A) Processing helix chain 'U' and resid 229 through 232 No H-bonds generated for 'chain 'U' and resid 229 through 232' Processing helix chain 'V' and resid 103 through 124 Processing helix chain 'V' and resid 130 through 143 Processing helix chain 'V' and resid 184 through 196 removed outlier: 3.807A pdb=" N ILE V 187 " --> pdb=" O SER V 184 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR V 190 " --> pdb=" O ILE V 187 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER V 191 " --> pdb=" O PHE V 188 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE V 193 " --> pdb=" O TYR V 190 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP V 194 " --> pdb=" O SER V 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA V 195 " --> pdb=" O PHE V 192 " (cutoff:3.500A) Processing helix chain 'V' and resid 203 through 220 removed outlier: 3.825A pdb=" N ARG V 220 " --> pdb=" O HIS V 216 " (cutoff:3.500A) Processing helix chain 'V' and resid 245 through 247 No H-bonds generated for 'chain 'V' and resid 245 through 247' Processing helix chain 'V' and resid 256 through 258 No H-bonds generated for 'chain 'V' and resid 256 through 258' Processing helix chain 'W' and resid 78 through 99 Processing helix chain 'W' and resid 105 through 118 Processing helix chain 'W' and resid 160 through 170 Processing helix chain 'W' and resid 177 through 194 Processing helix chain 'X' and resid 57 through 78 Processing helix chain 'X' and resid 84 through 98 removed outlier: 4.056A pdb=" N ALA X 98 " --> pdb=" O MET X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 153 removed outlier: 3.607A pdb=" N GLY X 148 " --> pdb=" O GLU X 144 " (cutoff:3.500A) Processing helix chain 'X' and resid 160 through 177 removed outlier: 3.664A pdb=" N ARG X 177 " --> pdb=" O SER X 173 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 71 Processing helix chain 'Y' and resid 79 through 95 removed outlier: 3.551A pdb=" N ILE Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG Y 95 " --> pdb=" O ALA Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 157 Processing helix chain 'Y' and resid 164 through 181 Processing helix chain 'Z' and resid 148 through 169 Processing helix chain 'Z' and resid 175 through 188 Processing helix chain 'Z' and resid 231 through 241 removed outlier: 4.085A pdb=" N GLY Z 236 " --> pdb=" O ILE Z 232 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL Z 237 " --> pdb=" O TYR Z 233 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR Z 240 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) Processing helix chain 'Z' and resid 248 through 263 Processing helix chain 'Z' and resid 291 through 298 removed outlier: 3.521A pdb=" N HIS Z 296 " --> pdb=" O THR Z 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 183 through 203 Processing helix chain 'a' and resid 211 through 225 removed outlier: 3.638A pdb=" N ARG a 225 " --> pdb=" O MET a 221 " (cutoff:3.500A) Processing helix chain 'a' and resid 268 through 280 Proline residue: a 273 - end of helix Processing helix chain 'a' and resid 294 through 311 Processing helix chain 'b' and resid 53 through 73 Processing helix chain 'b' and resid 81 through 97 Processing helix chain 'b' and resid 136 through 152 removed outlier: 3.584A pdb=" N ILE b 141 " --> pdb=" O GLY b 138 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ALA b 142 " --> pdb=" O ALA b 139 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU b 143 " --> pdb=" O TYR b 140 " (cutoff:3.500A) Proline residue: b 144 - end of helix removed outlier: 3.811A pdb=" N ARG b 147 " --> pdb=" O PRO b 144 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS b 152 " --> pdb=" O ALA b 149 " (cutoff:3.500A) Processing helix chain 'b' and resid 159 through 176 Processing helix chain 'b' and resid 209 through 211 No H-bonds generated for 'chain 'b' and resid 209 through 211' Processing helix chain 'b' and resid 213 through 216 No H-bonds generated for 'chain 'b' and resid 213 through 216' Processing sheet with id= A, first strand: chain 'A' and resid 167 through 171 removed outlier: 5.614A pdb=" N LEU A 35 " --> pdb=" O GLN A 50 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 162 through 165 removed outlier: 4.065A pdb=" N ILE A 153 " --> pdb=" O HIS A 165 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N CYS A 75 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLU A 68 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N MET A 77 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU A 66 " --> pdb=" O MET A 77 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 158 through 161 Processing sheet with id= D, first strand: chain 'B' and resid 153 through 155 removed outlier: 5.973A pdb=" N CYS B 72 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL B 65 " --> pdb=" O CYS B 72 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N TYR B 74 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 63 " --> pdb=" O TYR B 74 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 167 through 170 Processing sheet with id= F, first strand: chain 'C' and resid 162 through 165 removed outlier: 4.030A pdb=" N LEU C 153 " --> pdb=" O TRP C 165 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N CYS C 80 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS C 73 " --> pdb=" O CYS C 80 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL C 82 " --> pdb=" O MET C 71 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET C 71 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 158 through 161 Processing sheet with id= H, first strand: chain 'D' and resid 153 through 155 removed outlier: 6.443A pdb=" N LEU D 71 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS D 64 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N PHE D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE D 62 " --> pdb=" O PHE D 73 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 267 through 270 removed outlier: 4.719A pdb=" N VAL E 317 " --> pdb=" O TYR E 330 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 262 through 265 removed outlier: 4.048A pdb=" N LEU E 253 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA E 176 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLU E 169 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET E 178 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE E 167 " --> pdb=" O MET E 178 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 323 through 326 Processing sheet with id= L, first strand: chain 'F' and resid 318 through 321 removed outlier: 4.210A pdb=" N LEU F 309 " --> pdb=" O TYR F 321 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N MET F 237 " --> pdb=" O GLU F 230 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU F 230 " --> pdb=" O MET F 237 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE F 239 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL F 228 " --> pdb=" O ILE F 239 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 162 through 165 Processing sheet with id= N, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.974A pdb=" N ALA G 142 " --> pdb=" O GLY G 145 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU G 148 " --> pdb=" O TYR G 160 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 179 through 182 Processing sheet with id= P, first strand: chain 'H' and resid 175 through 177 removed outlier: 3.952A pdb=" N VAL H 165 " --> pdb=" O LEU H 177 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N CYS H 97 " --> pdb=" O LYS H 90 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LYS H 90 " --> pdb=" O CYS H 97 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ARG H 99 " --> pdb=" O LEU H 88 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU H 88 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 74 through 76 removed outlier: 6.506A pdb=" N SER H 76 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 153 through 157 Processing sheet with id= S, first strand: chain 'I' and resid 148 through 150 removed outlier: 5.921A pdb=" N CYS I 72 " --> pdb=" O TYR I 65 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N TYR I 65 " --> pdb=" O CYS I 72 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLY I 74 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE I 63 " --> pdb=" O GLY I 74 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 49 through 51 removed outlier: 3.556A pdb=" N ASP I 57 " --> pdb=" O ALA I 49 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU I 51 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL I 55 " --> pdb=" O GLU I 51 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 136 through 140 removed outlier: 5.981A pdb=" N SER J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N CYS J 19 " --> pdb=" O GLY J 16 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 119 through 123 removed outlier: 7.069A pdb=" N TYR J 51 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL J 44 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU J 53 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU J 42 " --> pdb=" O LEU J 53 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.631A pdb=" N GLU J 30 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR J 34 " --> pdb=" O GLU J 30 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 140 through 143 removed outlier: 3.992A pdb=" N TYR K 13 " --> pdb=" O CYS K 10 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL K 191 " --> pdb=" O ILE K 202 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 135 through 137 removed outlier: 6.656A pdb=" N VAL K 45 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLN K 38 " --> pdb=" O VAL K 45 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS K 47 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE K 36 " --> pdb=" O CYS K 47 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 22 through 24 removed outlier: 6.482A pdb=" N PHE K 24 " --> pdb=" O LYS K 28 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LYS K 28 " --> pdb=" O PHE K 24 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 224 through 227 removed outlier: 6.682A pdb=" N HIS L 277 " --> pdb=" O LYS L 285 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LYS L 285 " --> pdb=" O HIS L 277 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N HIS L 279 " --> pdb=" O TRP L 283 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N TRP L 283 " --> pdb=" O HIS L 279 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 133 through 135 removed outlier: 3.738A pdb=" N MET L 199 " --> pdb=" O THR L 143 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'L' and resid 119 through 121 removed outlier: 6.942A pdb=" N THR L 121 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE L 125 " --> pdb=" O THR L 121 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 261 through 265 removed outlier: 5.515A pdb=" N THR M 135 " --> pdb=" O ASP M 150 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 256 through 259 removed outlier: 4.053A pdb=" N GLU M 257 " --> pdb=" O SER M 249 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER M 249 " --> pdb=" O GLU M 257 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN M 234 " --> pdb=" O TYR M 250 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N MET M 177 " --> pdb=" O GLN M 170 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLN M 170 " --> pdb=" O MET M 177 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER M 179 " --> pdb=" O ILE M 168 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE M 168 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 132 through 135 Processing sheet with id= AG, first strand: chain 'N' and resid 39 through 41 Processing sheet with id= AH, first strand: chain 'N' and resid 24 through 26 removed outlier: 6.586A pdb=" N TYR N 26 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ALA N 30 " --> pdb=" O TYR N 26 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'O' and resid 167 through 171 removed outlier: 5.568A pdb=" N LEU O 35 " --> pdb=" O GLN O 50 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'O' and resid 162 through 165 removed outlier: 4.067A pdb=" N ILE O 153 " --> pdb=" O HIS O 165 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS O 75 " --> pdb=" O GLU O 68 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLU O 68 " --> pdb=" O CYS O 75 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N MET O 77 " --> pdb=" O LEU O 66 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU O 66 " --> pdb=" O MET O 77 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'P' and resid 158 through 161 removed outlier: 3.879A pdb=" N GLY P 41 " --> pdb=" O ALA P 38 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'P' and resid 153 through 155 removed outlier: 6.058A pdb=" N CYS P 72 " --> pdb=" O VAL P 65 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL P 65 " --> pdb=" O CYS P 72 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N TYR P 74 " --> pdb=" O VAL P 63 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL P 63 " --> pdb=" O TYR P 74 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'Q' and resid 167 through 170 removed outlier: 4.824A pdb=" N VAL Q 218 " --> pdb=" O LEU Q 249 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'Q' and resid 162 through 165 removed outlier: 4.017A pdb=" N LEU Q 153 " --> pdb=" O TRP Q 165 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N CYS Q 80 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS Q 73 " --> pdb=" O CYS Q 80 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL Q 82 " --> pdb=" O MET Q 71 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N MET Q 71 " --> pdb=" O VAL Q 82 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'R' and resid 158 through 161 Processing sheet with id= AP, first strand: chain 'R' and resid 62 through 64 Processing sheet with id= AQ, first strand: chain 'S' and resid 267 through 270 removed outlier: 4.727A pdb=" N VAL S 317 " --> pdb=" O TYR S 330 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'S' and resid 262 through 265 removed outlier: 4.072A pdb=" N LEU S 253 " --> pdb=" O TYR S 265 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA S 176 " --> pdb=" O GLU S 169 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU S 169 " --> pdb=" O ALA S 176 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N MET S 178 " --> pdb=" O ILE S 167 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE S 167 " --> pdb=" O MET S 178 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'T' and resid 323 through 326 Processing sheet with id= AT, first strand: chain 'T' and resid 318 through 321 removed outlier: 4.191A pdb=" N LEU T 309 " --> pdb=" O TYR T 321 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N MET T 237 " --> pdb=" O GLU T 230 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLU T 230 " --> pdb=" O MET T 237 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE T 239 " --> pdb=" O VAL T 228 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL T 228 " --> pdb=" O ILE T 239 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'U' and resid 162 through 165 Processing sheet with id= AV, first strand: chain 'U' and resid 157 through 160 removed outlier: 4.236A pdb=" N LEU U 148 " --> pdb=" O TYR U 160 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA U 142 " --> pdb=" O GLY U 145 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE U 76 " --> pdb=" O ALA U 69 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ALA U 69 " --> pdb=" O ILE U 76 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE U 78 " --> pdb=" O ILE U 67 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE U 67 " --> pdb=" O ILE U 78 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'V' and resid 179 through 182 Processing sheet with id= AX, first strand: chain 'V' and resid 175 through 177 removed outlier: 3.950A pdb=" N VAL V 165 " --> pdb=" O LEU V 177 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N CYS V 97 " --> pdb=" O LYS V 90 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LYS V 90 " --> pdb=" O CYS V 97 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ARG V 99 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU V 88 " --> pdb=" O ARG V 99 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'V' and resid 74 through 76 removed outlier: 6.593A pdb=" N SER V 76 " --> pdb=" O VAL V 80 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL V 80 " --> pdb=" O SER V 76 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'W' and resid 153 through 157 Processing sheet with id= BA, first strand: chain 'W' and resid 148 through 150 removed outlier: 5.912A pdb=" N CYS W 72 " --> pdb=" O TYR W 65 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR W 65 " --> pdb=" O CYS W 72 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLY W 74 " --> pdb=" O ILE W 63 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE W 63 " --> pdb=" O GLY W 74 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'W' and resid 49 through 51 removed outlier: 3.572A pdb=" N ASP W 57 " --> pdb=" O ALA W 49 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU W 51 " --> pdb=" O VAL W 55 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL W 55 " --> pdb=" O GLU W 51 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'X' and resid 136 through 140 removed outlier: 5.958A pdb=" N SER X 10 " --> pdb=" O ASP X 25 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N CYS X 19 " --> pdb=" O GLY X 16 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'X' and resid 119 through 123 removed outlier: 6.965A pdb=" N TYR X 51 " --> pdb=" O VAL X 44 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL X 44 " --> pdb=" O TYR X 51 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU X 53 " --> pdb=" O LEU X 42 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU X 42 " --> pdb=" O LEU X 53 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'X' and resid 28 through 30 removed outlier: 6.607A pdb=" N GLU X 30 " --> pdb=" O THR X 34 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N THR X 34 " --> pdb=" O GLU X 30 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'Y' and resid 140 through 143 removed outlier: 4.018A pdb=" N VAL Y 191 " --> pdb=" O ILE Y 202 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'Y' and resid 135 through 137 removed outlier: 6.669A pdb=" N VAL Y 45 " --> pdb=" O GLN Y 38 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLN Y 38 " --> pdb=" O VAL Y 45 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N CYS Y 47 " --> pdb=" O ILE Y 36 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE Y 36 " --> pdb=" O CYS Y 47 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'Y' and resid 22 through 24 removed outlier: 6.486A pdb=" N PHE Y 24 " --> pdb=" O LYS Y 28 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LYS Y 28 " --> pdb=" O PHE Y 24 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'Z' and resid 224 through 227 removed outlier: 6.651A pdb=" N HIS Z 277 " --> pdb=" O LYS Z 285 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LYS Z 285 " --> pdb=" O HIS Z 277 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N HIS Z 279 " --> pdb=" O TRP Z 283 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TRP Z 283 " --> pdb=" O HIS Z 279 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'Z' and resid 133 through 135 removed outlier: 3.750A pdb=" N MET Z 199 " --> pdb=" O THR Z 143 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'Z' and resid 119 through 121 removed outlier: 7.021A pdb=" N THR Z 121 " --> pdb=" O ILE Z 125 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE Z 125 " --> pdb=" O THR Z 121 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'a' and resid 261 through 265 removed outlier: 5.547A pdb=" N THR a 135 " --> pdb=" O ASP a 150 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'a' and resid 256 through 259 removed outlier: 4.058A pdb=" N GLU a 257 " --> pdb=" O SER a 249 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER a 249 " --> pdb=" O GLU a 257 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN a 234 " --> pdb=" O TYR a 250 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N MET a 177 " --> pdb=" O GLN a 170 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLN a 170 " --> pdb=" O MET a 177 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N SER a 179 " --> pdb=" O ILE a 168 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE a 168 " --> pdb=" O SER a 179 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'b' and resid 132 through 135 Processing sheet with id= BO, first strand: chain 'b' and resid 39 through 41 Processing sheet with id= BP, first strand: chain 'b' and resid 24 through 26 removed outlier: 6.531A pdb=" N TYR b 26 " --> pdb=" O ALA b 30 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ALA b 30 " --> pdb=" O TYR b 26 " (cutoff:3.500A) 2502 hydrogen bonds defined for protein. 7098 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: 23.80 Time building geometry restraints manager: 20.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8371 1.31 - 1.45: 13202 1.45 - 1.58: 28033 1.58 - 1.71: 0 1.71 - 1.85: 516 Bond restraints: 50122 Sorted by residual: bond pdb=" C PRO Y 53 " pdb=" O PRO Y 53 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.26e-02 6.30e+03 2.14e+01 bond pdb=" N ILE O 53 " pdb=" CA ILE O 53 " ideal model delta sigma weight residual 1.456 1.493 -0.037 8.60e-03 1.35e+04 1.88e+01 bond pdb=" N GLY D 37 " pdb=" CA GLY D 37 " ideal model delta sigma weight residual 1.442 1.475 -0.033 7.70e-03 1.69e+04 1.83e+01 bond pdb=" C PRO W 152 " pdb=" O PRO W 152 " ideal model delta sigma weight residual 1.238 1.186 0.052 1.22e-02 6.72e+03 1.83e+01 bond pdb=" C PRO K 53 " pdb=" O PRO K 53 " ideal model delta sigma weight residual 1.237 1.184 0.054 1.26e-02 6.30e+03 1.82e+01 ... (remaining 50117 not shown) Histogram of bond angle deviations from ideal: 95.40 - 103.24: 457 103.24 - 111.07: 16202 111.07 - 118.91: 28619 118.91 - 126.75: 22110 126.75 - 134.59: 422 Bond angle restraints: 67810 Sorted by residual: angle pdb=" C LEU E 138 " pdb=" N GLY E 139 " pdb=" CA GLY E 139 " ideal model delta sigma weight residual 121.65 126.78 -5.13 6.80e-01 2.16e+00 5.70e+01 angle pdb=" C THR M 232 " pdb=" CA THR M 232 " pdb=" CB THR M 232 " ideal model delta sigma weight residual 110.34 120.17 -9.83 1.40e+00 5.10e-01 4.94e+01 angle pdb=" C LEU S 138 " pdb=" N GLY S 139 " pdb=" CA GLY S 139 " ideal model delta sigma weight residual 122.18 126.74 -4.56 6.90e-01 2.10e+00 4.36e+01 angle pdb=" CA ASP N 21 " pdb=" CB ASP N 21 " pdb=" CG ASP N 21 " ideal model delta sigma weight residual 112.60 119.16 -6.56 1.00e+00 1.00e+00 4.31e+01 angle pdb=" C THR a 232 " pdb=" CA THR a 232 " pdb=" CB THR a 232 " ideal model delta sigma weight residual 110.94 118.94 -8.00 1.28e+00 6.10e-01 3.91e+01 ... (remaining 67805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 25843 18.03 - 36.05: 2922 36.05 - 54.08: 967 54.08 - 72.11: 287 72.11 - 90.14: 91 Dihedral angle restraints: 30110 sinusoidal: 11784 harmonic: 18326 Sorted by residual: dihedral pdb=" CA GLY Q 171 " pdb=" C GLY Q 171 " pdb=" N GLN Q 172 " pdb=" CA GLN Q 172 " ideal model delta harmonic sigma weight residual 180.00 -145.28 -34.72 0 5.00e+00 4.00e-02 4.82e+01 dihedral pdb=" CA GLY C 171 " pdb=" C GLY C 171 " pdb=" N GLN C 172 " pdb=" CA GLN C 172 " ideal model delta harmonic sigma weight residual -180.00 -145.84 -34.16 0 5.00e+00 4.00e-02 4.67e+01 dihedral pdb=" CA LYS J 204 " pdb=" C LYS J 204 " pdb=" N ASP J 205 " pdb=" CA ASP J 205 " ideal model delta harmonic sigma weight residual -180.00 -145.92 -34.08 0 5.00e+00 4.00e-02 4.65e+01 ... (remaining 30107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3248 0.063 - 0.126: 2872 0.126 - 0.189: 1173 0.189 - 0.252: 218 0.252 - 0.316: 33 Chirality restraints: 7544 Sorted by residual: chirality pdb=" CA ILE A 153 " pdb=" N ILE A 153 " pdb=" C ILE A 153 " pdb=" CB ILE A 153 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA THR Q 66 " pdb=" N THR Q 66 " pdb=" C THR Q 66 " pdb=" CB THR Q 66 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB THR K 82 " pdb=" CA THR K 82 " pdb=" OG1 THR K 82 " pdb=" CG2 THR K 82 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 7541 not shown) Planarity restraints: 8790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 J6E Z4000 " -0.051 2.00e-02 2.50e+03 1.14e-01 3.58e+02 pdb=" C11 J6E Z4000 " 0.120 2.00e-02 2.50e+03 pdb=" C12 J6E Z4000 " -0.068 2.00e-02 2.50e+03 pdb=" C13 J6E Z4000 " -0.123 2.00e-02 2.50e+03 pdb=" C14 J6E Z4000 " -0.082 2.00e-02 2.50e+03 pdb=" C15 J6E Z4000 " -0.121 2.00e-02 2.50e+03 pdb=" C16 J6E Z4000 " 0.028 2.00e-02 2.50e+03 pdb=" N2 J6E Z4000 " -0.059 2.00e-02 2.50e+03 pdb=" N3 J6E Z4000 " -0.038 2.00e-02 2.50e+03 pdb=" N4 J6E Z4000 " 0.164 2.00e-02 2.50e+03 pdb=" N5 J6E Z4000 " 0.229 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 J6E L4000 " -0.012 2.00e-02 2.50e+03 9.85e-02 2.67e+02 pdb=" C11 J6E L4000 " -0.098 2.00e-02 2.50e+03 pdb=" C12 J6E L4000 " 0.073 2.00e-02 2.50e+03 pdb=" C13 J6E L4000 " 0.119 2.00e-02 2.50e+03 pdb=" C14 J6E L4000 " 0.060 2.00e-02 2.50e+03 pdb=" C15 J6E L4000 " 0.076 2.00e-02 2.50e+03 pdb=" C16 J6E L4000 " 0.007 2.00e-02 2.50e+03 pdb=" N2 J6E L4000 " 0.071 2.00e-02 2.50e+03 pdb=" N3 J6E L4000 " 0.037 2.00e-02 2.50e+03 pdb=" N4 J6E L4000 " -0.114 2.00e-02 2.50e+03 pdb=" N5 J6E L4000 " -0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N J6E Z4000 " 0.105 2.00e-02 2.50e+03 1.00e-01 2.26e+02 pdb=" C J6E Z4000 " 0.064 2.00e-02 2.50e+03 pdb=" C1 J6E Z4000 " 0.067 2.00e-02 2.50e+03 pdb=" C10 J6E Z4000 " 0.024 2.00e-02 2.50e+03 pdb=" C11 J6E Z4000 " 0.117 2.00e-02 2.50e+03 pdb=" C2 J6E Z4000 " 0.013 2.00e-02 2.50e+03 pdb=" C3 J6E Z4000 " -0.096 2.00e-02 2.50e+03 pdb=" C9 J6E Z4000 " -0.193 2.00e-02 2.50e+03 pdb=" F J6E Z4000 " -0.101 2.00e-02 2.50e+03 ... (remaining 8787 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1953 2.70 - 3.25: 47314 3.25 - 3.80: 82694 3.80 - 4.35: 118784 4.35 - 4.90: 190159 Nonbonded interactions: 440904 Sorted by model distance: nonbonded pdb=" OG1 THR W 200 " pdb=" O HOH W 301 " model vdw 2.155 2.440 nonbonded pdb=" OE2 GLU E 205 " pdb=" OH TYR M 200 " model vdw 2.191 2.440 nonbonded pdb=" OE2 GLU S 205 " pdb=" OH TYR a 200 " model vdw 2.201 2.440 nonbonded pdb=" OE1 GLN A 195 " pdb=" NH1 ARG A 223 " model vdw 2.205 2.520 nonbonded pdb=" OE1 GLN O 195 " pdb=" NH1 ARG O 223 " model vdw 2.208 2.520 ... (remaining 440899 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } 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: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.000 Extract box with map and model: 7.730 Check model and map are aligned: 0.680 Set scattering table: 0.440 Process input model: 134.560 Find NCS groups from input model: 4.930 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.080 50122 Z= 0.814 Angle : 1.871 10.047 67810 Z= 1.372 Chirality : 0.095 0.316 7544 Planarity : 0.006 0.114 8790 Dihedral : 18.624 90.136 18402 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.94 % Favored : 95.71 % Rotamer: Outliers : 11.11 % Allowed : 10.39 % Favored : 78.50 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.09), residues: 6290 helix: -2.22 (0.08), residues: 2316 sheet: -1.09 (0.12), residues: 1534 loop : -1.45 (0.11), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.006 TRP H 245 HIS 0.013 0.003 HIS E 199 PHE 0.064 0.006 PHE Z 260 TYR 0.042 0.006 TYR R 110 ARG 0.010 0.001 ARG O 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1927 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 582 poor density : 1345 time to evaluate : 5.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8444 (mmmm) REVERT: A 42 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8061 (ptpt) REVERT: A 105 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8314 (tm-30) REVERT: A 125 GLN cc_start: 0.8221 (mt0) cc_final: 0.7627 (mm-40) REVERT: A 140 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8926 (mmp) REVERT: A 150 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8671 (pttm) REVERT: A 161 TRP cc_start: 0.8767 (t60) cc_final: 0.8451 (t-100) REVERT: A 184 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7559 (mmm160) REVERT: A 196 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8738 (tmtm) REVERT: A 197 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8251 (mt-10) REVERT: A 207 GLN cc_start: 0.8100 (mt0) cc_final: 0.7870 (mt0) REVERT: A 215 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8413 (mmmm) REVERT: A 217 LYS cc_start: 0.8599 (tttt) cc_final: 0.7876 (pttt) REVERT: B 3 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6965 (tp30) REVERT: B 31 THR cc_start: 0.9159 (p) cc_final: 0.8919 (t) REVERT: B 62 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8316 (mmmt) REVERT: B 87 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8565 (p) REVERT: B 118 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8038 (mt-10) REVERT: B 181 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7899 (mt-10) REVERT: B 182 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8623 (tp) REVERT: B 183 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7891 (mp0) REVERT: B 197 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: B 221 VAL cc_start: 0.7944 (m) cc_final: 0.7660 (t) REVERT: C 29 GLN cc_start: 0.8318 (mt0) cc_final: 0.8104 (mt0) REVERT: C 40 LYS cc_start: 0.8186 (mmtp) cc_final: 0.7760 (pttt) REVERT: C 130 TYR cc_start: 0.8911 (m-80) cc_final: 0.8582 (m-80) REVERT: C 161 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8022 (p0) REVERT: C 250 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8578 (m) REVERT: C 265 ARG cc_start: 0.7561 (tpp-160) cc_final: 0.7098 (tpt-90) REVERT: C 270 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6813 (mmtt) REVERT: D 4 ASP cc_start: 0.8367 (p0) cc_final: 0.8157 (p0) REVERT: D 52 LYS cc_start: 0.7705 (mttp) cc_final: 0.7420 (tptm) REVERT: D 61 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8481 (mmpt) REVERT: D 174 LYS cc_start: 0.8584 (mmmt) cc_final: 0.8286 (mtpt) REVERT: D 177 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8151 (mmtp) REVERT: D 178 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8124 (t70) REVERT: D 180 MET cc_start: 0.8346 (mtt) cc_final: 0.7947 (mtm) REVERT: D 215 ARG cc_start: 0.8395 (ttp-170) cc_final: 0.8038 (mtp-110) REVERT: D 224 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7948 (ptmt) REVERT: D 227 VAL cc_start: 0.8966 (t) cc_final: 0.8688 (p) REVERT: E 107 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6547 (mt-10) REVERT: E 109 ASP cc_start: 0.6384 (OUTLIER) cc_final: 0.5467 (m-30) REVERT: E 140 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8775 (mm) REVERT: E 171 ASP cc_start: 0.9112 (t0) cc_final: 0.8899 (t0) REVERT: E 190 GLU cc_start: 0.8464 (tp30) cc_final: 0.7961 (tp30) REVERT: E 220 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8766 (m) REVERT: E 221 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6546 (pp) REVERT: E 252 GLN cc_start: 0.8694 (mt0) cc_final: 0.8432 (mt0) REVERT: E 287 ARG cc_start: 0.8720 (ttp-110) cc_final: 0.8292 (mtt-85) REVERT: E 300 ASP cc_start: 0.8111 (m-30) cc_final: 0.7610 (m-30) REVERT: E 307 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6879 (pt0) REVERT: E 326 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8532 (mmtm) REVERT: E 328 HIS cc_start: 0.8373 (m-70) cc_final: 0.7910 (m-70) REVERT: E 342 MET cc_start: 0.6559 (OUTLIER) cc_final: 0.6140 (ttm) REVERT: F 203 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8871 (pttt) REVERT: F 220 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6761 (tp30) REVERT: F 221 LEU cc_start: 0.8087 (tt) cc_final: 0.7829 (tm) REVERT: F 237 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8816 (mtp) REVERT: F 270 MET cc_start: 0.9139 (mmm) cc_final: 0.8863 (mmm) REVERT: F 273 MET cc_start: 0.9089 (ttm) cc_final: 0.8753 (ttp) REVERT: F 276 MET cc_start: 0.8509 (mtt) cc_final: 0.8306 (mtm) REVERT: F 322 LYS cc_start: 0.8889 (mttp) cc_final: 0.8646 (mttt) REVERT: F 369 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7271 (mm-30) REVERT: F 371 ASN cc_start: 0.8466 (p0) cc_final: 0.8258 (p0) REVERT: F 382 LYS cc_start: 0.8806 (ttpp) cc_final: 0.8559 (ttpt) REVERT: F 395 ARG cc_start: 0.7530 (mtp180) cc_final: 0.7325 (mtm-85) REVERT: F 402 LYS cc_start: 0.7176 (tttp) cc_final: 0.6888 (tppt) REVERT: G 13 ASP cc_start: 0.8693 (p0) cc_final: 0.8462 (p0) REVERT: G 43 LYS cc_start: 0.8609 (mmtp) cc_final: 0.8014 (mtmt) REVERT: G 51 GLU cc_start: 0.8290 (tt0) cc_final: 0.8034 (pp20) REVERT: G 205 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7326 (ttmt) REVERT: G 231 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7477 (mpt) REVERT: H 105 ASP cc_start: 0.8890 (m-30) cc_final: 0.8583 (m-30) REVERT: H 123 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8339 (p0) REVERT: H 137 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.8878 (t80) REVERT: H 143 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7983 (mmp) REVERT: H 201 MET cc_start: 0.8877 (mtt) cc_final: 0.8618 (mtt) REVERT: H 234 ASP cc_start: 0.8680 (p0) cc_final: 0.8455 (p0) REVERT: H 274 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8828 (mt) REVERT: H 279 MET cc_start: 0.8890 (mtp) cc_final: 0.8673 (mtp) REVERT: I 66 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8742 (mmt) REVERT: I 71 MET cc_start: 0.9038 (mmm) cc_final: 0.8725 (mmt) REVERT: I 81 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.8923 (m) REVERT: I 85 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8773 (p) REVERT: I 118 ARG cc_start: 0.8818 (ttm170) cc_final: 0.8468 (mtm-85) REVERT: I 209 LYS cc_start: 0.9032 (tptt) cc_final: 0.8471 (tptt) REVERT: I 213 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: I 225 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6998 (mmp) REVERT: I 232 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7981 (mm) REVERT: J 4 MET cc_start: 0.9101 (mmm) cc_final: 0.8841 (mmt) REVERT: J 25 ASP cc_start: 0.8995 (p0) cc_final: 0.8744 (p0) REVERT: J 38 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8521 (mm-30) REVERT: J 75 LYS cc_start: 0.9141 (tmtm) cc_final: 0.8596 (tptt) REVERT: J 79 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8327 (mt-10) REVERT: J 81 ASP cc_start: 0.8731 (m-30) cc_final: 0.8423 (m-30) REVERT: J 90 MET cc_start: 0.9267 (ttp) cc_final: 0.9059 (ttt) REVERT: J 97 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8218 (mt-10) REVERT: J 114 LYS cc_start: 0.8035 (tttt) cc_final: 0.7545 (tppt) REVERT: J 193 ASP cc_start: 0.8190 (t70) cc_final: 0.7973 (t0) REVERT: J 201 LYS cc_start: 0.8938 (tttp) cc_final: 0.8567 (tptp) REVERT: K 1 MET cc_start: 0.7937 (mmm) cc_final: 0.7107 (mmm) REVERT: K 13 TYR cc_start: 0.9143 (p90) cc_final: 0.8887 (p90) REVERT: K 62 LYS cc_start: 0.8935 (tttm) cc_final: 0.8727 (tttm) REVERT: K 115 SER cc_start: 0.9120 (p) cc_final: 0.8893 (p) REVERT: K 129 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8351 (mtp) REVERT: K 145 TYR cc_start: 0.9187 (m-10) cc_final: 0.8883 (m-10) REVERT: K 163 SER cc_start: 0.8536 (OUTLIER) cc_final: 0.8310 (m) REVERT: K 200 GLU cc_start: 0.8920 (pt0) cc_final: 0.8637 (pt0) REVERT: K 206 HIS cc_start: 0.8279 (p90) cc_final: 0.7954 (p90) REVERT: L 155 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8690 (mt-10) REVERT: L 249 GLU cc_start: 0.8572 (tp30) cc_final: 0.8035 (mp0) REVERT: M 143 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8274 (p0) REVERT: M 152 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8565 (ttm170) REVERT: M 154 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8780 (p0) REVERT: M 174 TYR cc_start: 0.8704 (m-10) cc_final: 0.7992 (m-10) REVERT: M 182 MET cc_start: 0.9125 (ttt) cc_final: 0.8745 (ttt) REVERT: M 240 ASP cc_start: 0.8479 (p0) cc_final: 0.8221 (p0) REVERT: M 241 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7320 (mm-30) REVERT: M 311 ARG cc_start: 0.9168 (mmt180) cc_final: 0.8707 (mmt180) REVERT: M 317 ASP cc_start: 0.8358 (m-30) cc_final: 0.8098 (m-30) REVERT: M 337 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8540 (mtt-85) REVERT: M 338 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8306 (mmtp) REVERT: N 64 GLU cc_start: 0.8715 (tt0) cc_final: 0.8506 (tt0) REVERT: N 69 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8400 (mpt180) REVERT: N 96 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8980 (ppt170) REVERT: N 100 ASP cc_start: 0.8533 (t70) cc_final: 0.8171 (t0) REVERT: N 151 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8111 (pt0) REVERT: N 163 MET cc_start: 0.9024 (tpp) cc_final: 0.8818 (mmm) REVERT: N 179 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8631 (mtt-85) REVERT: N 183 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8437 (tppt) REVERT: N 211 TYR cc_start: 0.9207 (m-10) cc_final: 0.8797 (m-10) REVERT: O 42 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8440 (ptmt) REVERT: O 53 ILE cc_start: 0.8788 (pt) cc_final: 0.8461 (mm) REVERT: O 67 TYR cc_start: 0.9222 (m-80) cc_final: 0.8951 (m-80) REVERT: O 93 GLU cc_start: 0.8401 (tt0) cc_final: 0.8060 (mt-10) REVERT: O 115 MET cc_start: 0.9295 (mmm) cc_final: 0.9008 (mmp) REVERT: O 125 GLN cc_start: 0.8550 (mt0) cc_final: 0.8216 (mm-40) REVERT: O 193 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9029 (mt) REVERT: O 217 LYS cc_start: 0.8303 (tttt) cc_final: 0.7979 (pttm) REVERT: P 3 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6617 (tt0) REVERT: P 16 LYS cc_start: 0.8960 (ptmt) cc_final: 0.8258 (mmtm) REVERT: P 39 THR cc_start: 0.8826 (p) cc_final: 0.8414 (m) REVERT: P 42 VAL cc_start: 0.9446 (OUTLIER) cc_final: 0.9245 (p) REVERT: P 47 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8966 (ptmt) REVERT: P 62 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8362 (mmmt) REVERT: P 74 TYR cc_start: 0.9277 (p90) cc_final: 0.9065 (p90) REVERT: P 90 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8673 (tttm) REVERT: P 154 TRP cc_start: 0.7929 (m100) cc_final: 0.7035 (m-90) REVERT: P 167 ASP cc_start: 0.8411 (m-30) cc_final: 0.7963 (m-30) REVERT: P 174 LYS cc_start: 0.8283 (mttm) cc_final: 0.8071 (mtpp) REVERT: P 179 ASP cc_start: 0.7958 (m-30) cc_final: 0.7735 (m-30) REVERT: P 181 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7971 (mt-10) REVERT: P 197 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.6922 (t80) REVERT: P 201 MET cc_start: 0.8784 (mtm) cc_final: 0.8425 (mtm) REVERT: P 202 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8626 (t) REVERT: P 205 ASN cc_start: 0.8478 (t0) cc_final: 0.8228 (t0) REVERT: P 226 ASP cc_start: 0.7879 (m-30) cc_final: 0.7371 (t70) REVERT: Q 15 GLU cc_start: 0.8194 (tt0) cc_final: 0.7982 (mm-30) REVERT: Q 29 GLN cc_start: 0.8468 (mt0) cc_final: 0.8194 (mm110) REVERT: Q 64 LYS cc_start: 0.8475 (mmtm) cc_final: 0.8268 (mmtt) REVERT: Q 174 ASP cc_start: 0.7883 (p0) cc_final: 0.7272 (p0) REVERT: Q 182 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7638 (mttm) REVERT: Q 200 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8299 (mtp-110) REVERT: Q 204 LYS cc_start: 0.8548 (tttt) cc_final: 0.7867 (tptp) REVERT: Q 214 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8534 (m-30) REVERT: Q 237 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8439 (tptp) REVERT: Q 250 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8462 (p) REVERT: R 23 GLN cc_start: 0.8266 (mt0) cc_final: 0.7998 (mm-40) REVERT: R 47 LYS cc_start: 0.8448 (mttt) cc_final: 0.8244 (mtmm) REVERT: R 54 GLN cc_start: 0.8325 (pt0) cc_final: 0.7587 (mm-40) REVERT: R 60 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7837 (mpt90) REVERT: R 146 LYS cc_start: 0.8956 (tttm) cc_final: 0.8722 (tttp) REVERT: R 175 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8467 (t) REVERT: R 187 HIS cc_start: 0.8953 (t70) cc_final: 0.8718 (t-90) REVERT: R 213 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7902 (mp0) REVERT: R 218 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8273 (p) REVERT: R 219 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7672 (mm-30) REVERT: R 223 GLN cc_start: 0.7261 (mt0) cc_final: 0.7029 (tm-30) REVERT: R 232 GLU cc_start: 0.6996 (tt0) cc_final: 0.6618 (mt-10) REVERT: S 110 ARG cc_start: 0.7577 (mtt180) cc_final: 0.6724 (ptp-110) REVERT: S 221 ILE cc_start: 0.6611 (OUTLIER) cc_final: 0.6152 (pp) REVERT: S 248 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7935 (mm-30) REVERT: S 249 LYS cc_start: 0.8592 (mmtm) cc_final: 0.8183 (mmmt) REVERT: S 257 ASP cc_start: 0.8728 (m-30) cc_final: 0.8490 (m-30) REVERT: S 306 MET cc_start: 0.8470 (ptm) cc_final: 0.8223 (ptp) REVERT: S 336 LYS cc_start: 0.8097 (tttt) cc_final: 0.7582 (tppp) REVERT: T 169 GLU cc_start: 0.7613 (pm20) cc_final: 0.7323 (pt0) REVERT: T 205 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8389 (ttpp) REVERT: T 215 ARG cc_start: 0.7191 (ttt180) cc_final: 0.6892 (ttp-110) REVERT: T 220 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.6034 (mm-30) REVERT: T 237 MET cc_start: 0.9024 (ttp) cc_final: 0.8678 (ttp) REVERT: T 266 ASN cc_start: 0.8932 (t0) cc_final: 0.8657 (t0) REVERT: T 279 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8058 (mm-30) REVERT: T 343 HIS cc_start: 0.7299 (m90) cc_final: 0.7037 (m-70) REVERT: T 347 CYS cc_start: 0.8878 (m) cc_final: 0.8490 (m) REVERT: T 358 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8593 (mttp) REVERT: T 373 LYS cc_start: 0.8345 (ptpt) cc_final: 0.7843 (mmtp) REVERT: T 395 ARG cc_start: 0.7409 (mtp180) cc_final: 0.7184 (mtm-85) REVERT: T 396 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7853 (ttmt) REVERT: T 404 ARG cc_start: 0.5848 (OUTLIER) cc_final: 0.5395 (ppt170) REVERT: U 13 ASP cc_start: 0.8434 (p0) cc_final: 0.8231 (p0) REVERT: U 25 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8542 (mt-10) REVERT: U 29 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8372 (mttt) REVERT: U 86 ARG cc_start: 0.8954 (mtp180) cc_final: 0.8743 (mmm-85) REVERT: U 94 GLN cc_start: 0.8516 (tt0) cc_final: 0.8131 (tm-30) REVERT: U 115 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8657 (mmp80) REVERT: U 120 MET cc_start: 0.9106 (mtp) cc_final: 0.8906 (mtm) REVERT: U 141 TYR cc_start: 0.9396 (t80) cc_final: 0.9149 (t80) REVERT: U 192 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8059 (mttp) REVERT: U 203 LYS cc_start: 0.7938 (mttt) cc_final: 0.7445 (mtmm) REVERT: U 210 GLU cc_start: 0.8450 (pt0) cc_final: 0.8240 (pt0) REVERT: V 102 SER cc_start: 0.8599 (t) cc_final: 0.8260 (t) REVERT: V 139 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8355 (tptp) REVERT: V 140 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8579 (mtp) REVERT: V 143 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8067 (mmp) REVERT: V 201 MET cc_start: 0.8782 (mtt) cc_final: 0.8551 (mtm) REVERT: V 204 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8813 (p) REVERT: V 274 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8815 (mt) REVERT: W 61 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7596 (mtt180) REVERT: W 66 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8883 (mmt) REVERT: W 119 TYR cc_start: 0.9156 (m-80) cc_final: 0.8939 (m-80) REVERT: W 175 MET cc_start: 0.9391 (mtm) cc_final: 0.9138 (mtm) REVERT: W 182 GLU cc_start: 0.8674 (tp30) cc_final: 0.8380 (mm-30) REVERT: W 247 GLN cc_start: 0.8461 (mm110) cc_final: 0.8224 (mm-40) REVERT: X 6 TYR cc_start: 0.9021 (t80) cc_final: 0.8776 (t80) REVERT: X 12 MET cc_start: 0.9051 (tmm) cc_final: 0.8843 (tmm) REVERT: X 17 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8604 (ttmm) REVERT: X 30 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8416 (mt-10) REVERT: X 31 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8137 (mm-40) REVERT: X 38 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8567 (mm-30) REVERT: X 72 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8282 (mm-30) REVERT: X 93 SER cc_start: 0.9119 (OUTLIER) cc_final: 0.8687 (p) REVERT: X 99 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8678 (mmm160) REVERT: X 113 ASP cc_start: 0.8692 (t70) cc_final: 0.8444 (t70) REVERT: X 134 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8262 (pm20) REVERT: Y 1 MET cc_start: 0.7482 (mmm) cc_final: 0.7080 (mmm) REVERT: Y 15 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8833 (ttm) REVERT: Y 38 GLN cc_start: 0.9187 (tt0) cc_final: 0.8979 (tt0) REVERT: Y 40 ASP cc_start: 0.8564 (t0) cc_final: 0.8357 (t70) REVERT: Y 88 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8551 (t0) REVERT: Y 129 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8805 (mtm) REVERT: Y 156 ARG cc_start: 0.8979 (tpt-90) cc_final: 0.8688 (tpt90) REVERT: Y 200 GLU cc_start: 0.8755 (pt0) cc_final: 0.8256 (pm20) REVERT: Z 166 GLU cc_start: 0.8573 (tt0) cc_final: 0.8347 (tt0) REVERT: Z 194 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8811 (mt) REVERT: Z 196 MET cc_start: 0.9088 (ptm) cc_final: 0.8847 (ptp) REVERT: Z 244 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8302 (mmmt) REVERT: Z 280 GLU cc_start: 0.8305 (pt0) cc_final: 0.7870 (pm20) REVERT: Z 281 LYS cc_start: 0.8601 (mttm) cc_final: 0.8321 (mtmt) REVERT: a 131 ASP cc_start: 0.9160 (t0) cc_final: 0.8805 (t70) REVERT: a 152 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8558 (ttm170) REVERT: a 159 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8925 (pp) REVERT: a 192 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8386 (mmp) REVERT: a 226 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8537 (ptm160) REVERT: a 231 TYR cc_start: 0.9035 (t80) cc_final: 0.8777 (t80) REVERT: a 292 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8432 (ttp) REVERT: a 295 GLU cc_start: 0.8481 (mp0) cc_final: 0.8260 (mp0) REVERT: a 310 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8588 (mm-30) REVERT: a 312 ASP cc_start: 0.8561 (t0) cc_final: 0.8336 (t0) REVERT: a 337 ARG cc_start: 0.8867 (mtt-85) cc_final: 0.8642 (mtp85) REVERT: b 39 ARG cc_start: 0.8592 (ttm170) cc_final: 0.8264 (ttm170) REVERT: b 71 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8327 (ttpt) REVERT: b 77 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.7934 (m-30) REVERT: b 94 GLN cc_start: 0.8760 (tp40) cc_final: 0.8467 (tp-100) REVERT: b 96 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8866 (ppt170) REVERT: b 115 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7579 (tm-30) REVERT: b 122 ASP cc_start: 0.8647 (m-30) cc_final: 0.8409 (m-30) REVERT: b 151 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: b 179 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8810 (mmt90) outliers start: 582 outliers final: 150 residues processed: 1727 average time/residue: 1.7565 time to fit residues: 3705.4369 Evaluate side-chains 1257 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1003 time to evaluate : 5.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 149 PRO Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain D residue 12 PRO Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain H residue 173 SER Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 274 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 172 LYS Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 192 LYS Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 218 SER Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 152 ARG Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 159 LEU Chi-restraints excluded: chain M residue 219 SER Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 241 GLU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain M residue 337 ARG Chi-restraints excluded: chain M residue 338 LYS Chi-restraints excluded: chain N residue 3 SER Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 183 LYS Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 233 ARG Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 47 LYS Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 90 LYS Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 182 LYS Chi-restraints excluded: chain Q residue 200 ARG Chi-restraints excluded: chain Q residue 211 ILE Chi-restraints excluded: chain Q residue 214 ASP Chi-restraints excluded: chain Q residue 237 LYS Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 221 ILE Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 319 VAL Chi-restraints excluded: chain T residue 172 SER Chi-restraints excluded: chain T residue 220 GLU Chi-restraints excluded: chain T residue 235 VAL Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 358 LYS Chi-restraints excluded: chain T residue 362 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 396 LYS Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 192 LYS Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 123 ASP Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 140 MET Chi-restraints excluded: chain V residue 143 MET Chi-restraints excluded: chain V residue 173 SER Chi-restraints excluded: chain V residue 204 SER Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 274 ILE Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain W residue 167 LEU Chi-restraints excluded: chain W residue 237 THR Chi-restraints excluded: chain X residue 30 GLU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 99 ARG Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 15 MET Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 88 ASN Chi-restraints excluded: chain Y residue 97 ARG Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 129 MET Chi-restraints excluded: chain Y residue 181 ARG Chi-restraints excluded: chain Z residue 102 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 144 LEU Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 218 SER Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain a residue 143 ASP Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 152 ARG Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 167 LYS Chi-restraints excluded: chain a residue 192 MET Chi-restraints excluded: chain a residue 226 ARG Chi-restraints excluded: chain a residue 292 MET Chi-restraints excluded: chain a residue 310 GLU Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 96 ARG Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 179 ARG Chi-restraints excluded: chain b residue 192 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 520 optimal weight: 0.8980 chunk 466 optimal weight: 0.9980 chunk 259 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 314 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 482 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 293 optimal weight: 5.9990 chunk 359 optimal weight: 4.9990 chunk 559 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN B 100 ASN B 107 GLN B 117 GLN B 121 GLN B 187 HIS B 230 GLN C 239 HIS C 257 HIS C 263 GLN D 115 GLN D 120 GLN D 223 GLN E 255 GLN E 278 GLN F 195 ASN F 225 GLN F 259 ASN F 286 GLN F 305 GLN F 311 GLN G 8 HIS G 147 GLN H 246 ASN H 266 GLN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 166 GLN I 201 GLN J 26 ASN J 65 ASN K 73 HIS K 84 ASN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 GLN K 186 ASN L 222 GLN L 291 GLN M 130 GLN M 180 ASN M 188 GLN M 204 ASN M 234 ASN M 330 GLN N 70 GLN N 75 ASN N 205 HIS O 174 GLN O 207 GLN O 228 ASN P 19 GLN P 94 GLN P 100 ASN P 117 GLN P 121 GLN P 223 GLN P 230 GLN Q 20 GLN Q 239 HIS R 18 GLN R 92 GLN R 115 GLN R 187 HIS S 314 ASN T 206 ASN ** T 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 305 GLN T 331 GLN U 8 HIS U 54 HIS V 147 ASN V 241 GLN V 246 ASN W 86 ASN W 95 HIS W 102 GLN W 166 GLN W 247 GLN X 26 ASN X 65 ASN X 68 GLN ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 ASN Y 72 GLN Y 84 ASN Y 165 GLN Y 186 ASN ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN a 130 GLN a 180 ASN a 188 GLN a 234 ASN b 62 GLN b 70 GLN b 105 GLN Total number of N/Q/H flips: 91 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 50122 Z= 0.201 Angle : 0.565 10.065 67810 Z= 0.306 Chirality : 0.043 0.164 7544 Planarity : 0.004 0.043 8790 Dihedral : 10.871 95.171 7583 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.73 % Favored : 98.11 % Rotamer: Outliers : 6.45 % Allowed : 17.39 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.10), residues: 6290 helix: 0.96 (0.10), residues: 2320 sheet: -0.43 (0.12), residues: 1560 loop : -0.59 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 154 HIS 0.007 0.001 HIS F 234 PHE 0.019 0.002 PHE Y 8 TYR 0.017 0.001 TYR W 119 ARG 0.006 0.001 ARG M 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1445 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1107 time to evaluate : 5.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8322 (mmmm) REVERT: A 42 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7783 (ptmm) REVERT: A 53 ILE cc_start: 0.8773 (pt) cc_final: 0.8445 (pp) REVERT: A 105 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8246 (tm-30) REVERT: A 115 MET cc_start: 0.9113 (mmm) cc_final: 0.8894 (mmm) REVERT: A 125 GLN cc_start: 0.8190 (mt0) cc_final: 0.7659 (mm-40) REVERT: A 161 TRP cc_start: 0.8728 (t60) cc_final: 0.8425 (t-100) REVERT: A 184 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7558 (mmm160) REVERT: A 215 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8020 (mmmt) REVERT: A 217 LYS cc_start: 0.8636 (tttt) cc_final: 0.7975 (pttp) REVERT: B 118 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8216 (mt-10) REVERT: B 179 ASP cc_start: 0.8361 (m-30) cc_final: 0.8039 (m-30) REVERT: B 181 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7731 (mt-10) REVERT: B 197 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.6752 (m-80) REVERT: C 29 GLN cc_start: 0.8213 (mt0) cc_final: 0.7980 (mt0) REVERT: C 40 LYS cc_start: 0.8339 (mmtp) cc_final: 0.7845 (pttt) REVERT: C 130 TYR cc_start: 0.8624 (m-80) cc_final: 0.8362 (m-80) REVERT: C 207 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8205 (t0) REVERT: C 237 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8132 (tppt) REVERT: C 265 ARG cc_start: 0.7606 (tpp-160) cc_final: 0.7161 (tpt-90) REVERT: C 270 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6799 (mmtt) REVERT: D 4 ASP cc_start: 0.8378 (p0) cc_final: 0.8058 (p0) REVERT: D 52 LYS cc_start: 0.7925 (mttp) cc_final: 0.7610 (mppt) REVERT: D 57 ARG cc_start: 0.7711 (tmm160) cc_final: 0.7289 (ptt90) REVERT: D 61 LYS cc_start: 0.8757 (mptp) cc_final: 0.8446 (mmpt) REVERT: D 121 SER cc_start: 0.8885 (m) cc_final: 0.8643 (p) REVERT: D 174 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8304 (mtpt) REVERT: D 177 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7957 (mmtp) REVERT: D 178 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8063 (t70) REVERT: D 180 MET cc_start: 0.8324 (mtt) cc_final: 0.7968 (mtm) REVERT: D 215 ARG cc_start: 0.8435 (ttp-170) cc_final: 0.8035 (mtp-110) REVERT: D 221 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7067 (tp30) REVERT: D 224 LYS cc_start: 0.8235 (mtmt) cc_final: 0.7806 (ttpt) REVERT: D 232 GLU cc_start: 0.7401 (tt0) cc_final: 0.7074 (mt-10) REVERT: E 107 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6511 (mm-30) REVERT: E 109 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6009 (m-30) REVERT: E 190 GLU cc_start: 0.8389 (tp30) cc_final: 0.7924 (tp30) REVERT: E 283 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: E 287 ARG cc_start: 0.8763 (ttp-110) cc_final: 0.8484 (ttm110) REVERT: E 300 ASP cc_start: 0.7955 (m-30) cc_final: 0.7516 (m-30) REVERT: E 326 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8272 (mmtm) REVERT: E 328 HIS cc_start: 0.8475 (m-70) cc_final: 0.8117 (m-70) REVERT: E 342 MET cc_start: 0.6172 (ttm) cc_final: 0.5828 (ttm) REVERT: F 221 LEU cc_start: 0.7964 (tt) cc_final: 0.7717 (tm) REVERT: F 270 MET cc_start: 0.9008 (mmm) cc_final: 0.8657 (mmm) REVERT: G 13 ASP cc_start: 0.8678 (p0) cc_final: 0.8342 (p0) REVERT: G 43 LYS cc_start: 0.8618 (mmtp) cc_final: 0.8390 (mmmt) REVERT: G 51 GLU cc_start: 0.8263 (tt0) cc_final: 0.7779 (pp20) REVERT: G 115 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8253 (mmt90) REVERT: G 231 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7236 (mpt) REVERT: H 139 LYS cc_start: 0.8828 (ttmm) cc_final: 0.8441 (ttpp) REVERT: H 143 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.8000 (tpp) REVERT: H 201 MET cc_start: 0.8974 (mtt) cc_final: 0.8659 (mtt) REVERT: I 51 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7867 (tp30) REVERT: I 71 MET cc_start: 0.8763 (mmm) cc_final: 0.8475 (mmp) REVERT: I 118 ARG cc_start: 0.8841 (ttm170) cc_final: 0.8545 (ttp-110) REVERT: I 213 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: J 4 MET cc_start: 0.9131 (mmm) cc_final: 0.8907 (mmt) REVERT: J 38 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8544 (mm-30) REVERT: J 48 SER cc_start: 0.9079 (p) cc_final: 0.8846 (m) REVERT: J 79 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: J 97 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8225 (mt-10) REVERT: J 114 LYS cc_start: 0.7930 (tttt) cc_final: 0.7516 (tppt) REVERT: J 198 ARG cc_start: 0.9112 (mtt90) cc_final: 0.8911 (mtt180) REVERT: J 201 LYS cc_start: 0.9111 (tttp) cc_final: 0.8600 (ttpt) REVERT: K 1 MET cc_start: 0.7795 (mmm) cc_final: 0.7113 (mmm) REVERT: K 13 TYR cc_start: 0.9036 (p90) cc_final: 0.8755 (p90) REVERT: K 196 LYS cc_start: 0.8695 (ptmm) cc_final: 0.8467 (ptmm) REVERT: K 200 GLU cc_start: 0.8976 (pt0) cc_final: 0.8633 (pt0) REVERT: K 203 THR cc_start: 0.8255 (m) cc_final: 0.8040 (p) REVERT: K 206 HIS cc_start: 0.8234 (p90) cc_final: 0.7976 (p90) REVERT: L 134 LEU cc_start: 0.9142 (tt) cc_final: 0.8469 (mp) REVERT: L 155 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: L 191 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.7810 (m110) REVERT: L 249 GLU cc_start: 0.8623 (tp30) cc_final: 0.7962 (mp0) REVERT: M 130 GLN cc_start: 0.8512 (tt0) cc_final: 0.8291 (tt0) REVERT: M 174 TYR cc_start: 0.8710 (m-10) cc_final: 0.7924 (m-10) REVERT: M 182 MET cc_start: 0.9003 (ttt) cc_final: 0.8718 (ttt) REVERT: M 226 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7125 (ptp-170) REVERT: M 281 ARG cc_start: 0.8506 (mtp85) cc_final: 0.7785 (mtp-110) REVERT: M 330 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7459 (tm130) REVERT: M 337 ARG cc_start: 0.8768 (mtt-85) cc_final: 0.8531 (ttt-90) REVERT: N 34 ASN cc_start: 0.9183 (p0) cc_final: 0.8933 (p0) REVERT: N 69 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8383 (mpt180) REVERT: N 72 MET cc_start: 0.9112 (ttm) cc_final: 0.8760 (ttm) REVERT: N 100 ASP cc_start: 0.8104 (t70) cc_final: 0.7803 (t0) REVERT: N 151 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: N 163 MET cc_start: 0.8991 (tpp) cc_final: 0.8718 (mmm) REVERT: N 179 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8557 (mtt90) REVERT: N 183 LYS cc_start: 0.8974 (ttpt) cc_final: 0.8518 (tppt) REVERT: N 203 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: O 7 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7294 (p0) REVERT: O 67 TYR cc_start: 0.9040 (m-80) cc_final: 0.8775 (m-80) REVERT: O 90 ARG cc_start: 0.8691 (mmp80) cc_final: 0.8465 (mmp80) REVERT: O 93 GLU cc_start: 0.8232 (tt0) cc_final: 0.7643 (mt-10) REVERT: O 115 MET cc_start: 0.9175 (mmm) cc_final: 0.8946 (mmp) REVERT: O 125 GLN cc_start: 0.8386 (mt0) cc_final: 0.8145 (mm-40) REVERT: O 140 MET cc_start: 0.9376 (mmm) cc_final: 0.8929 (mmp) REVERT: O 161 TRP cc_start: 0.8634 (t60) cc_final: 0.8379 (t-100) REVERT: O 186 LYS cc_start: 0.8473 (mttt) cc_final: 0.8229 (mttt) REVERT: O 190 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8311 (mp) REVERT: O 217 LYS cc_start: 0.8444 (tttt) cc_final: 0.8154 (pttp) REVERT: P 16 LYS cc_start: 0.8937 (ptmt) cc_final: 0.8164 (mmtt) REVERT: P 39 THR cc_start: 0.8855 (p) cc_final: 0.8422 (m) REVERT: P 90 LYS cc_start: 0.8891 (ttmt) cc_final: 0.8676 (tttm) REVERT: P 100 ASN cc_start: 0.8612 (t0) cc_final: 0.8379 (t0) REVERT: P 154 TRP cc_start: 0.8025 (m100) cc_final: 0.6943 (m-90) REVERT: P 197 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7055 (t80) REVERT: P 202 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8604 (t) REVERT: P 226 ASP cc_start: 0.7870 (m-30) cc_final: 0.7556 (t70) REVERT: Q 15 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: Q 190 THR cc_start: 0.8757 (p) cc_final: 0.8524 (p) REVERT: Q 193 ASP cc_start: 0.8524 (t0) cc_final: 0.8270 (m-30) REVERT: Q 204 LYS cc_start: 0.8349 (tttt) cc_final: 0.7826 (tptp) REVERT: R 23 GLN cc_start: 0.8108 (mt0) cc_final: 0.7857 (mm-40) REVERT: R 54 GLN cc_start: 0.8367 (pt0) cc_final: 0.7636 (tp40) REVERT: R 60 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7932 (mpt90) REVERT: R 152 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8588 (tmt) REVERT: R 203 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7971 (m110) REVERT: R 206 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8123 (tt) REVERT: R 213 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7896 (mp0) REVERT: R 218 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8320 (p) REVERT: R 220 GLU cc_start: 0.7536 (pm20) cc_final: 0.7230 (pm20) REVERT: R 231 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6794 (pttp) REVERT: S 110 ARG cc_start: 0.7525 (mtt180) cc_final: 0.6901 (mtm110) REVERT: S 118 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8324 (mp0) REVERT: S 187 ILE cc_start: 0.9104 (mm) cc_final: 0.8871 (mm) REVERT: S 249 LYS cc_start: 0.8604 (mmtm) cc_final: 0.8213 (mmmt) REVERT: S 289 MET cc_start: 0.9030 (mtt) cc_final: 0.8771 (mtp) REVERT: S 300 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8134 (m-30) REVERT: S 306 MET cc_start: 0.8133 (ptm) cc_final: 0.7908 (ptp) REVERT: S 309 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8423 (mm-40) REVERT: S 336 LYS cc_start: 0.8095 (tttt) cc_final: 0.7605 (tppp) REVERT: T 190 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7699 (m-40) REVERT: T 195 ASN cc_start: 0.8729 (m-40) cc_final: 0.8418 (m-40) REVERT: T 279 GLU cc_start: 0.8216 (mm-30) cc_final: 0.8007 (mm-30) REVERT: T 343 HIS cc_start: 0.7265 (m90) cc_final: 0.6941 (m-70) REVERT: T 347 CYS cc_start: 0.8722 (m) cc_final: 0.8369 (m) REVERT: T 401 PHE cc_start: 0.7551 (t80) cc_final: 0.7257 (t80) REVERT: T 404 ARG cc_start: 0.5859 (OUTLIER) cc_final: 0.5311 (ppt170) REVERT: U 61 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8301 (tptp) REVERT: U 86 ARG cc_start: 0.8757 (mtp180) cc_final: 0.8557 (mmm-85) REVERT: U 94 GLN cc_start: 0.8549 (tt0) cc_final: 0.8189 (tm-30) REVERT: U 115 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8304 (mmt90) REVERT: U 120 MET cc_start: 0.9084 (mtp) cc_final: 0.8859 (mtt) REVERT: U 156 THR cc_start: 0.9263 (m) cc_final: 0.9050 (m) REVERT: U 203 LYS cc_start: 0.7947 (mttt) cc_final: 0.7426 (mtmm) REVERT: V 121 GLN cc_start: 0.8855 (tt0) cc_final: 0.8653 (tt0) REVERT: V 140 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8499 (mtp) REVERT: V 143 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8155 (mmp) REVERT: V 201 MET cc_start: 0.8765 (mtt) cc_final: 0.8478 (mtm) REVERT: V 273 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8226 (tppt) REVERT: W 61 ARG cc_start: 0.7779 (mtp85) cc_final: 0.7440 (mmt180) REVERT: W 87 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8275 (ptm) REVERT: W 119 TYR cc_start: 0.8976 (m-80) cc_final: 0.8760 (m-80) REVERT: W 149 ASP cc_start: 0.8228 (m-30) cc_final: 0.7970 (m-30) REVERT: W 213 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8356 (tm-30) REVERT: X 6 TYR cc_start: 0.9032 (t80) cc_final: 0.8762 (t80) REVERT: X 31 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8088 (mm-40) REVERT: X 38 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8577 (mm-30) REVERT: X 134 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8284 (pm20) REVERT: X 192 LYS cc_start: 0.9152 (mtmp) cc_final: 0.8939 (mtpt) REVERT: Y 11 LYS cc_start: 0.8510 (tttm) cc_final: 0.8255 (tppt) REVERT: Y 38 GLN cc_start: 0.9191 (tt0) cc_final: 0.8930 (tt0) REVERT: Y 118 ASP cc_start: 0.8907 (t0) cc_final: 0.8692 (t0) REVERT: Y 200 GLU cc_start: 0.8744 (pt0) cc_final: 0.8220 (pm20) REVERT: Z 131 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8168 (mmt) REVERT: Z 166 GLU cc_start: 0.8696 (tt0) cc_final: 0.8434 (tt0) REVERT: Z 191 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.7900 (m110) REVERT: Z 194 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8406 (mp) REVERT: Z 244 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8440 (mttm) REVERT: Z 281 LYS cc_start: 0.8651 (mttm) cc_final: 0.8313 (mtmt) REVERT: Z 285 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.8909 (ttpt) REVERT: Z 291 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8669 (pp30) REVERT: a 152 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.8669 (ttm170) REVERT: a 201 LYS cc_start: 0.8836 (mtpm) cc_final: 0.8522 (ttpm) REVERT: a 242 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7979 (mm-30) REVERT: a 251 ASP cc_start: 0.8901 (p0) cc_final: 0.8495 (p0) REVERT: a 255 SER cc_start: 0.8904 (t) cc_final: 0.8546 (p) REVERT: a 295 GLU cc_start: 0.8390 (mp0) cc_final: 0.8140 (mp0) REVERT: a 337 ARG cc_start: 0.8872 (mtt-85) cc_final: 0.8604 (mtp85) REVERT: b 77 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: b 115 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7681 (tm-30) REVERT: b 151 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: b 179 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8689 (mmt90) outliers start: 338 outliers final: 110 residues processed: 1315 average time/residue: 1.7286 time to fit residues: 2796.0144 Evaluate side-chains 1115 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 946 time to evaluate : 5.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 152 ARG Chi-restraints excluded: chain M residue 159 LEU Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 330 GLN Chi-restraints excluded: chain N residue 3 SER Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 172 GLN Chi-restraints excluded: chain Q residue 187 GLU Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 231 LYS Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 300 ASP Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 61 LYS Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 140 MET Chi-restraints excluded: chain V residue 143 MET Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain W residue 210 ASP Chi-restraints excluded: chain W residue 213 GLU Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain Z residue 245 ASP Chi-restraints excluded: chain Z residue 285 LYS Chi-restraints excluded: chain Z residue 291 GLN Chi-restraints excluded: chain a residue 152 ARG Chi-restraints excluded: chain a residue 253 VAL Chi-restraints excluded: chain a residue 327 ASP Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 179 ARG Chi-restraints excluded: chain b residue 192 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 310 optimal weight: 0.9990 chunk 173 optimal weight: 0.3980 chunk 465 optimal weight: 0.8980 chunk 380 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 560 optimal weight: 2.9990 chunk 605 optimal weight: 0.7980 chunk 499 optimal weight: 3.9990 chunk 555 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 449 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 100 ASN C 62 GLN D 97 ASN D 187 HIS E 113 ASN F 190 ASN F 225 GLN F 259 ASN G 8 HIS G 98 ASN G 147 GLN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 31 GLN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 GLN L 123 GLN L 222 GLN L 291 GLN M 154 ASN M 180 ASN M 234 ASN N 70 GLN O 228 ASN O 236 ASN P 19 GLN Q 20 GLN R 143 HIS T 266 ASN ** T 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 305 GLN V 241 GLN V 246 ASN ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 180 ASN a 234 ASN b 105 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 50122 Z= 0.221 Angle : 0.522 9.313 67810 Z= 0.280 Chirality : 0.042 0.165 7544 Planarity : 0.004 0.049 8790 Dihedral : 8.502 88.353 7249 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.78 % Favored : 98.09 % Rotamer: Outliers : 5.31 % Allowed : 19.63 % Favored : 75.07 % 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: 0.65 (0.10), residues: 6290 helix: 1.70 (0.10), residues: 2344 sheet: -0.19 (0.12), residues: 1584 loop : -0.29 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 165 HIS 0.007 0.001 HIS R 187 PHE 0.018 0.002 PHE Y 8 TYR 0.015 0.001 TYR B 116 ARG 0.009 0.000 ARG b 195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1301 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1023 time to evaluate : 5.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ILE cc_start: 0.8789 (pt) cc_final: 0.8471 (pp) REVERT: A 105 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8331 (tm-30) REVERT: A 125 GLN cc_start: 0.8180 (mt0) cc_final: 0.7676 (mm-40) REVERT: A 161 TRP cc_start: 0.8741 (t60) cc_final: 0.8301 (t-100) REVERT: A 184 ARG cc_start: 0.7707 (tpp80) cc_final: 0.7476 (mmm160) REVERT: A 215 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8148 (mmtt) REVERT: A 217 LYS cc_start: 0.8614 (tttt) cc_final: 0.7981 (pttp) REVERT: B 3 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.5452 (tm-30) REVERT: B 16 LYS cc_start: 0.8584 (ptmt) cc_final: 0.8316 (ptmm) REVERT: B 87 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8454 (m) REVERT: B 118 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8140 (tt0) REVERT: B 179 ASP cc_start: 0.8249 (m-30) cc_final: 0.7971 (m-30) REVERT: B 184 ASP cc_start: 0.7733 (t0) cc_final: 0.7408 (m-30) REVERT: B 210 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8421 (ptt90) REVERT: C 40 LYS cc_start: 0.8423 (mmtp) cc_final: 0.7906 (pttt) REVERT: C 130 TYR cc_start: 0.8540 (m-80) cc_final: 0.8301 (m-80) REVERT: C 237 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8273 (tppt) REVERT: C 265 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7336 (tpt-90) REVERT: D 4 ASP cc_start: 0.8369 (p0) cc_final: 0.8106 (p0) REVERT: D 52 LYS cc_start: 0.7943 (mttp) cc_final: 0.7635 (mppt) REVERT: D 57 ARG cc_start: 0.7682 (tmm160) cc_final: 0.7299 (ptt90) REVERT: D 61 LYS cc_start: 0.8762 (mptp) cc_final: 0.8452 (mmpt) REVERT: D 100 ASP cc_start: 0.9006 (m-30) cc_final: 0.8779 (m-30) REVERT: D 121 SER cc_start: 0.8804 (m) cc_final: 0.8571 (p) REVERT: D 177 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8022 (mmtp) REVERT: D 178 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8117 (t70) REVERT: D 180 MET cc_start: 0.8314 (mtt) cc_final: 0.7953 (mtm) REVERT: D 215 ARG cc_start: 0.8430 (ttp-170) cc_final: 0.7984 (mtp-110) REVERT: D 221 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7102 (tp30) REVERT: D 232 GLU cc_start: 0.7298 (tt0) cc_final: 0.6786 (mt-10) REVERT: E 107 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: E 178 MET cc_start: 0.8514 (ptp) cc_final: 0.8216 (mtm) REVERT: E 190 GLU cc_start: 0.8356 (tp30) cc_final: 0.8043 (tp30) REVERT: E 300 ASP cc_start: 0.8000 (m-30) cc_final: 0.7540 (m-30) REVERT: E 326 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8277 (mmtm) REVERT: E 328 HIS cc_start: 0.8471 (m-70) cc_final: 0.8207 (m90) REVERT: E 342 MET cc_start: 0.6272 (ttm) cc_final: 0.5881 (ttm) REVERT: F 220 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6787 (tp30) REVERT: F 221 LEU cc_start: 0.7833 (tt) cc_final: 0.7562 (tm) REVERT: F 270 MET cc_start: 0.9041 (mmm) cc_final: 0.8609 (mmm) REVERT: F 402 LYS cc_start: 0.7060 (mmtm) cc_final: 0.6816 (mmmt) REVERT: G 13 ASP cc_start: 0.8668 (p0) cc_final: 0.8259 (p0) REVERT: G 43 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8427 (mmmt) REVERT: G 44 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: G 51 GLU cc_start: 0.8250 (tt0) cc_final: 0.7834 (tm-30) REVERT: G 115 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8235 (mpt-90) REVERT: G 231 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7179 (mpt) REVERT: H 139 LYS cc_start: 0.8793 (ttmm) cc_final: 0.8373 (ttpp) REVERT: H 143 MET cc_start: 0.8209 (ttp) cc_final: 0.7994 (tpp) REVERT: H 201 MET cc_start: 0.8958 (mtt) cc_final: 0.8715 (mtt) REVERT: H 279 MET cc_start: 0.8987 (mtm) cc_final: 0.8491 (mtp) REVERT: I 118 ARG cc_start: 0.8854 (ttm170) cc_final: 0.8566 (ttp-110) REVERT: I 225 MET cc_start: 0.7423 (mtp) cc_final: 0.7046 (mtt) REVERT: I 226 TYR cc_start: 0.7040 (t80) cc_final: 0.6381 (t80) REVERT: I 229 GLN cc_start: 0.7497 (mm110) cc_final: 0.6896 (mm110) REVERT: I 230 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: J 4 MET cc_start: 0.9117 (mmm) cc_final: 0.8863 (mmt) REVERT: J 38 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8548 (mm-30) REVERT: J 79 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: J 97 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8204 (mt-10) REVERT: J 114 LYS cc_start: 0.8029 (tttt) cc_final: 0.7539 (tppt) REVERT: J 201 LYS cc_start: 0.9096 (tttp) cc_final: 0.8565 (ttpt) REVERT: K 1 MET cc_start: 0.7554 (mmm) cc_final: 0.7031 (mmm) REVERT: K 70 MET cc_start: 0.8921 (mpp) cc_final: 0.8671 (tpp) REVERT: K 196 LYS cc_start: 0.8689 (ptmm) cc_final: 0.8481 (ptmm) REVERT: K 200 GLU cc_start: 0.8979 (pt0) cc_final: 0.8616 (pt0) REVERT: K 206 HIS cc_start: 0.8193 (p90) cc_final: 0.7983 (p90) REVERT: L 134 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8436 (mp) REVERT: L 155 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: L 190 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7410 (ptp90) REVERT: L 191 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.7818 (m110) REVERT: L 249 GLU cc_start: 0.8605 (tp30) cc_final: 0.7968 (mp0) REVERT: M 152 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8467 (ttm170) REVERT: M 174 TYR cc_start: 0.8739 (m-10) cc_final: 0.7853 (m-10) REVERT: M 212 LYS cc_start: 0.9045 (tttm) cc_final: 0.8787 (ttpp) REVERT: M 226 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7322 (ptp-170) REVERT: M 281 ARG cc_start: 0.8541 (mtp85) cc_final: 0.7869 (mtp-110) REVERT: M 332 GLU cc_start: 0.8282 (pt0) cc_final: 0.8064 (pt0) REVERT: M 337 ARG cc_start: 0.8656 (mtt-85) cc_final: 0.8352 (ttt-90) REVERT: N 34 ASN cc_start: 0.9240 (p0) cc_final: 0.8979 (p0) REVERT: N 69 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8330 (mpt180) REVERT: N 100 ASP cc_start: 0.8016 (t70) cc_final: 0.7724 (t0) REVERT: N 106 MET cc_start: 0.8849 (mpt) cc_final: 0.8232 (mpt) REVERT: N 151 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: N 179 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8602 (mtt90) REVERT: N 183 LYS cc_start: 0.8981 (ttpt) cc_final: 0.8562 (tppt) REVERT: N 195 ARG cc_start: 0.8757 (mtp-110) cc_final: 0.8341 (mtp180) REVERT: N 203 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: O 7 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7304 (p0) REVERT: O 36 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8742 (t) REVERT: O 67 TYR cc_start: 0.8987 (m-80) cc_final: 0.8722 (m-80) REVERT: O 93 GLU cc_start: 0.8151 (tt0) cc_final: 0.7712 (tm-30) REVERT: O 97 ASP cc_start: 0.8278 (m-30) cc_final: 0.7949 (m-30) REVERT: O 115 MET cc_start: 0.9207 (mmm) cc_final: 0.8979 (mmp) REVERT: O 125 GLN cc_start: 0.8347 (mt0) cc_final: 0.8129 (mm-40) REVERT: O 140 MET cc_start: 0.9356 (mmm) cc_final: 0.8842 (mmp) REVERT: O 186 LYS cc_start: 0.8450 (mttt) cc_final: 0.8217 (mttt) REVERT: O 190 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8422 (mp) REVERT: O 217 LYS cc_start: 0.8466 (tttt) cc_final: 0.8170 (pttp) REVERT: P 16 LYS cc_start: 0.8887 (ptmt) cc_final: 0.8144 (mmtt) REVERT: P 85 ILE cc_start: 0.9190 (mt) cc_final: 0.8899 (mt) REVERT: P 100 ASN cc_start: 0.8630 (t0) cc_final: 0.8420 (t0) REVERT: P 154 TRP cc_start: 0.7913 (m100) cc_final: 0.6847 (m-90) REVERT: P 197 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.6868 (t80) REVERT: P 202 THR cc_start: 0.8869 (p) cc_final: 0.8551 (t) REVERT: P 226 ASP cc_start: 0.7884 (m-30) cc_final: 0.7643 (t70) REVERT: Q 15 GLU cc_start: 0.8156 (tt0) cc_final: 0.7885 (tt0) REVERT: Q 29 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8085 (mp10) REVERT: Q 53 HIS cc_start: 0.8640 (t-90) cc_final: 0.8190 (t-90) REVERT: Q 193 ASP cc_start: 0.8475 (t0) cc_final: 0.8189 (m-30) REVERT: Q 200 ARG cc_start: 0.8621 (mtm110) cc_final: 0.8329 (mtp-110) REVERT: Q 204 LYS cc_start: 0.8562 (tttt) cc_final: 0.8116 (tptp) REVERT: R 23 GLN cc_start: 0.8131 (mt0) cc_final: 0.7873 (mm-40) REVERT: R 49 SER cc_start: 0.6243 (t) cc_final: 0.5801 (p) REVERT: R 54 GLN cc_start: 0.8339 (pt0) cc_final: 0.7535 (mm110) REVERT: R 60 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7877 (mpt90) REVERT: R 152 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8602 (tmt) REVERT: R 195 GLU cc_start: 0.8104 (tp30) cc_final: 0.7897 (mm-30) REVERT: R 213 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7903 (mp0) REVERT: R 218 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8323 (p) REVERT: S 110 ARG cc_start: 0.7556 (mtt180) cc_final: 0.6857 (mtm110) REVERT: S 118 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8344 (mp0) REVERT: S 249 LYS cc_start: 0.8712 (mmtm) cc_final: 0.8332 (mmmt) REVERT: S 336 LYS cc_start: 0.8041 (tttt) cc_final: 0.7578 (tppp) REVERT: T 190 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7718 (m-40) REVERT: T 279 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7900 (mm-30) REVERT: T 290 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8457 (mttt) REVERT: T 343 HIS cc_start: 0.7277 (m90) cc_final: 0.6934 (m-70) REVERT: T 347 CYS cc_start: 0.8713 (m) cc_final: 0.8393 (m) REVERT: T 395 ARG cc_start: 0.7198 (mtm-85) cc_final: 0.6880 (mtm-85) REVERT: T 404 ARG cc_start: 0.5821 (OUTLIER) cc_final: 0.5399 (ppt170) REVERT: U 94 GLN cc_start: 0.8569 (tt0) cc_final: 0.8247 (tm-30) REVERT: U 203 LYS cc_start: 0.7975 (mttt) cc_final: 0.7459 (mtmm) REVERT: V 121 GLN cc_start: 0.8906 (tt0) cc_final: 0.8662 (tt0) REVERT: V 140 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8504 (mtp) REVERT: V 143 MET cc_start: 0.8520 (ttp) cc_final: 0.8114 (mmp) REVERT: V 201 MET cc_start: 0.8813 (mtt) cc_final: 0.8580 (mtm) REVERT: V 273 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8283 (tptt) REVERT: W 61 ARG cc_start: 0.7757 (mtp85) cc_final: 0.7493 (mmt90) REVERT: W 82 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: W 87 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8411 (ptm) REVERT: W 213 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8335 (tm-30) REVERT: X 6 TYR cc_start: 0.9058 (t80) cc_final: 0.8788 (t80) REVERT: X 17 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8621 (ttmm) REVERT: X 31 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8051 (mm-40) REVERT: X 38 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8568 (mm-30) REVERT: X 79 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8672 (mt-10) REVERT: X 134 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8249 (pm20) REVERT: Y 38 GLN cc_start: 0.9203 (tt0) cc_final: 0.8950 (tt0) REVERT: Y 40 ASP cc_start: 0.8648 (t0) cc_final: 0.8393 (t70) REVERT: Y 200 GLU cc_start: 0.8822 (pt0) cc_final: 0.8431 (pt0) REVERT: Z 131 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8169 (mmt) REVERT: Z 166 GLU cc_start: 0.8690 (tt0) cc_final: 0.8446 (tt0) REVERT: Z 191 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.7981 (m110) REVERT: Z 194 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8340 (mp) REVERT: Z 244 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8272 (mmtt) REVERT: Z 281 LYS cc_start: 0.8697 (mttm) cc_final: 0.8316 (mtmt) REVERT: a 201 LYS cc_start: 0.8806 (mtpm) cc_final: 0.8514 (ttpm) REVERT: a 242 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8105 (mm-30) REVERT: a 292 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8437 (tpp) REVERT: a 295 GLU cc_start: 0.8472 (mp0) cc_final: 0.8188 (mp0) REVERT: a 310 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8707 (tp30) REVERT: a 337 ARG cc_start: 0.8763 (mtt-85) cc_final: 0.8481 (mtm180) REVERT: b 77 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8319 (m-30) REVERT: b 115 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7759 (tm-30) REVERT: b 179 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8698 (mmt90) outliers start: 278 outliers final: 125 residues processed: 1192 average time/residue: 1.7407 time to fit residues: 2551.9093 Evaluate side-chains 1137 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 960 time to evaluate : 5.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 190 ARG Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 152 ARG Chi-restraints excluded: chain M residue 159 LEU Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 290 LYS Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 182 SER Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 140 MET Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 241 GLN Chi-restraints excluded: chain V residue 252 MET Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain W residue 175 MET Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 210 ASP Chi-restraints excluded: chain W residue 213 GLU Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 152 GLN Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain Z residue 245 ASP Chi-restraints excluded: chain Z residue 249 GLU Chi-restraints excluded: chain a residue 154 ASN Chi-restraints excluded: chain a residue 253 VAL Chi-restraints excluded: chain a residue 292 MET Chi-restraints excluded: chain a residue 293 THR Chi-restraints excluded: chain a residue 310 GLU Chi-restraints excluded: chain a residue 327 ASP Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 179 ARG Chi-restraints excluded: chain b residue 192 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 553 optimal weight: 1.9990 chunk 421 optimal weight: 9.9990 chunk 290 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 376 optimal weight: 0.7980 chunk 562 optimal weight: 3.9990 chunk 595 optimal weight: 9.9990 chunk 293 optimal weight: 4.9990 chunk 533 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 228 ASN B 100 ASN B 205 ASN C 62 GLN F 371 ASN G 98 ASN G 147 GLN I 247 GLN J 31 GLN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 GLN L 123 GLN L 222 GLN L 291 GLN M 130 GLN N 70 GLN O 228 ASN Q 257 HIS S 255 GLN T 195 ASN ** T 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 246 ASN ** W 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN a 180 ASN b 105 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 50122 Z= 0.321 Angle : 0.550 9.689 67810 Z= 0.292 Chirality : 0.044 0.168 7544 Planarity : 0.004 0.051 8790 Dihedral : 7.960 89.064 7186 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.92 % Favored : 97.95 % Rotamer: Outliers : 5.63 % Allowed : 20.14 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.10), residues: 6290 helix: 1.76 (0.10), residues: 2350 sheet: -0.14 (0.12), residues: 1580 loop : -0.19 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 165 HIS 0.008 0.001 HIS R 187 PHE 0.017 0.002 PHE K 8 TYR 0.016 0.002 TYR K 128 ARG 0.008 0.001 ARG N 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 966 time to evaluate : 5.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ILE cc_start: 0.8777 (pt) cc_final: 0.8455 (pp) REVERT: A 105 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8314 (tm-30) REVERT: A 115 MET cc_start: 0.9204 (mmm) cc_final: 0.8983 (mmm) REVERT: A 125 GLN cc_start: 0.8157 (mt0) cc_final: 0.7715 (mm-40) REVERT: A 161 TRP cc_start: 0.8753 (t60) cc_final: 0.8297 (t-100) REVERT: A 184 ARG cc_start: 0.8023 (tpp80) cc_final: 0.7481 (mmm160) REVERT: A 215 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8098 (mmmt) REVERT: A 217 LYS cc_start: 0.8664 (tttt) cc_final: 0.8006 (pttp) REVERT: B 3 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6018 (tt0) REVERT: B 16 LYS cc_start: 0.8608 (ptmt) cc_final: 0.8250 (ptmt) REVERT: B 118 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8168 (tt0) REVERT: B 184 ASP cc_start: 0.7853 (t0) cc_final: 0.7557 (m-30) REVERT: B 210 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8443 (ptt90) REVERT: C 40 LYS cc_start: 0.8451 (mmtp) cc_final: 0.7863 (pttt) REVERT: C 119 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8529 (tt) REVERT: C 130 TYR cc_start: 0.8530 (m-80) cc_final: 0.8248 (m-80) REVERT: C 196 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8817 (tt) REVERT: C 237 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8289 (tppt) REVERT: C 265 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7289 (tpt-90) REVERT: D 4 ASP cc_start: 0.8265 (p0) cc_final: 0.8064 (p0) REVERT: D 52 LYS cc_start: 0.7973 (mttp) cc_final: 0.7606 (mppt) REVERT: D 57 ARG cc_start: 0.7808 (tmm160) cc_final: 0.7289 (ptt90) REVERT: D 61 LYS cc_start: 0.8823 (mptp) cc_final: 0.8512 (mmpt) REVERT: D 121 SER cc_start: 0.8847 (m) cc_final: 0.8626 (p) REVERT: D 177 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8040 (mmtp) REVERT: D 180 MET cc_start: 0.8298 (mtt) cc_final: 0.7915 (mtm) REVERT: D 215 ARG cc_start: 0.8402 (ttp-170) cc_final: 0.7973 (mtp-110) REVERT: D 221 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7207 (tp30) REVERT: D 232 GLU cc_start: 0.7203 (tt0) cc_final: 0.6723 (mt-10) REVERT: E 140 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8687 (mm) REVERT: E 190 GLU cc_start: 0.8409 (tp30) cc_final: 0.7996 (tp30) REVERT: E 283 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: E 300 ASP cc_start: 0.7982 (m-30) cc_final: 0.7469 (m-30) REVERT: E 326 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8311 (mmtm) REVERT: E 329 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8597 (mtt) REVERT: E 342 MET cc_start: 0.6519 (ttm) cc_final: 0.6091 (ttm) REVERT: F 221 LEU cc_start: 0.7856 (tt) cc_final: 0.7631 (tm) REVERT: F 270 MET cc_start: 0.9099 (mmm) cc_final: 0.8706 (mmm) REVERT: F 402 LYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6771 (mmmt) REVERT: G 44 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8146 (m-30) REVERT: G 51 GLU cc_start: 0.8214 (tt0) cc_final: 0.7949 (tt0) REVERT: G 115 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8256 (mpt-90) REVERT: G 182 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.8342 (p) REVERT: H 139 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8423 (ttpp) REVERT: H 143 MET cc_start: 0.8236 (ttp) cc_final: 0.8001 (tpp) REVERT: H 201 MET cc_start: 0.8975 (mtt) cc_final: 0.8745 (mtt) REVERT: H 279 MET cc_start: 0.8989 (mtm) cc_final: 0.8491 (mtp) REVERT: I 118 ARG cc_start: 0.8850 (ttm170) cc_final: 0.8573 (ttp-110) REVERT: I 225 MET cc_start: 0.7509 (mtp) cc_final: 0.7114 (mtt) REVERT: I 226 TYR cc_start: 0.7128 (t80) cc_final: 0.6436 (t80) REVERT: I 229 GLN cc_start: 0.7625 (mm110) cc_final: 0.7031 (mm110) REVERT: I 230 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: J 4 MET cc_start: 0.9157 (mmm) cc_final: 0.8902 (mmt) REVERT: J 38 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8583 (mm-30) REVERT: J 79 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: J 97 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8223 (mt-10) REVERT: J 114 LYS cc_start: 0.8006 (tttt) cc_final: 0.7535 (tppt) REVERT: K 1 MET cc_start: 0.7630 (mmm) cc_final: 0.7144 (mmm) REVERT: K 22 ASN cc_start: 0.8937 (t0) cc_final: 0.8695 (t0) REVERT: K 196 LYS cc_start: 0.8756 (ptmm) cc_final: 0.8527 (ptmm) REVERT: K 200 GLU cc_start: 0.8920 (pt0) cc_final: 0.8573 (pt0) REVERT: K 206 HIS cc_start: 0.8176 (p90) cc_final: 0.7953 (p90) REVERT: L 155 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: L 191 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.7792 (m110) REVERT: M 174 TYR cc_start: 0.8772 (m-10) cc_final: 0.8040 (m-10) REVERT: M 201 LYS cc_start: 0.8671 (mtpm) cc_final: 0.8384 (mtpp) REVERT: M 212 LYS cc_start: 0.9052 (tttm) cc_final: 0.8812 (ttpp) REVERT: M 257 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8721 (pt0) REVERT: M 281 ARG cc_start: 0.8590 (mtp85) cc_final: 0.7940 (mtp-110) REVERT: N 69 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8324 (mpt180) REVERT: N 72 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8866 (ttm) REVERT: N 106 MET cc_start: 0.8853 (mpt) cc_final: 0.8213 (mpt) REVERT: N 151 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: N 179 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8644 (mtt-85) REVERT: N 183 LYS cc_start: 0.8975 (ttpt) cc_final: 0.8726 (tppp) REVERT: N 203 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: O 7 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7283 (p0) REVERT: O 36 THR cc_start: 0.8976 (p) cc_final: 0.8751 (t) REVERT: O 67 TYR cc_start: 0.8996 (m-80) cc_final: 0.8697 (m-80) REVERT: O 93 GLU cc_start: 0.8155 (tt0) cc_final: 0.7642 (tm-30) REVERT: O 97 ASP cc_start: 0.8298 (m-30) cc_final: 0.7907 (m-30) REVERT: O 115 MET cc_start: 0.9236 (mmm) cc_final: 0.8960 (mmp) REVERT: O 125 GLN cc_start: 0.8356 (mt0) cc_final: 0.8120 (tt0) REVERT: O 173 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7876 (mmpt) REVERT: O 190 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8404 (mp) REVERT: O 217 LYS cc_start: 0.8355 (tttt) cc_final: 0.8154 (pttp) REVERT: O 236 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8194 (m110) REVERT: P 16 LYS cc_start: 0.8875 (ptmt) cc_final: 0.8077 (mmtt) REVERT: P 100 ASN cc_start: 0.8665 (t0) cc_final: 0.8445 (t0) REVERT: P 154 TRP cc_start: 0.7920 (m100) cc_final: 0.6938 (m-90) REVERT: P 202 THR cc_start: 0.8952 (p) cc_final: 0.8618 (t) REVERT: P 226 ASP cc_start: 0.7885 (m-30) cc_final: 0.7684 (t70) REVERT: Q 15 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: Q 29 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8117 (mp10) REVERT: Q 53 HIS cc_start: 0.8703 (t-90) cc_final: 0.8273 (t-90) REVERT: Q 193 ASP cc_start: 0.8470 (t0) cc_final: 0.8176 (m-30) REVERT: Q 204 LYS cc_start: 0.8570 (tttt) cc_final: 0.8148 (tptp) REVERT: Q 266 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6583 (tm-30) REVERT: R 23 GLN cc_start: 0.8231 (mt0) cc_final: 0.7920 (mm-40) REVERT: R 49 SER cc_start: 0.6361 (t) cc_final: 0.5861 (p) REVERT: R 54 GLN cc_start: 0.8283 (pt0) cc_final: 0.7528 (mm110) REVERT: R 60 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7834 (mpt90) REVERT: R 213 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7909 (mp0) REVERT: R 218 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8404 (p) REVERT: S 118 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: S 249 LYS cc_start: 0.8754 (mmtm) cc_final: 0.8351 (mmmt) REVERT: S 336 LYS cc_start: 0.8030 (tttt) cc_final: 0.7585 (tppp) REVERT: T 190 ASN cc_start: 0.8075 (OUTLIER) cc_final: 0.7739 (m-40) REVERT: T 279 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8034 (mm-30) REVERT: T 343 HIS cc_start: 0.7283 (m90) cc_final: 0.6950 (m-70) REVERT: T 347 CYS cc_start: 0.8787 (m) cc_final: 0.8419 (m) REVERT: T 395 ARG cc_start: 0.7138 (mtm-85) cc_final: 0.6712 (mtm-85) REVERT: T 404 ARG cc_start: 0.5504 (OUTLIER) cc_final: 0.5115 (ppt170) REVERT: U 94 GLN cc_start: 0.8598 (tt0) cc_final: 0.8263 (tm-30) REVERT: U 114 ASN cc_start: 0.8935 (m-40) cc_final: 0.8682 (m110) REVERT: U 203 LYS cc_start: 0.7924 (mttt) cc_final: 0.7399 (mtmm) REVERT: V 140 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8471 (mtp) REVERT: V 143 MET cc_start: 0.8506 (ttp) cc_final: 0.8147 (mmp) REVERT: V 201 MET cc_start: 0.8830 (mtt) cc_final: 0.8528 (mtm) REVERT: V 273 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8094 (tppt) REVERT: W 61 ARG cc_start: 0.7733 (mtp85) cc_final: 0.7370 (mmt180) REVERT: W 82 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: X 6 TYR cc_start: 0.9049 (t80) cc_final: 0.8720 (t80) REVERT: X 17 LYS cc_start: 0.8910 (ttpt) cc_final: 0.8615 (ttmm) REVERT: X 31 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8074 (mm-40) REVERT: X 38 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8604 (mm-30) REVERT: X 79 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8673 (mt-10) REVERT: X 94 MET cc_start: 0.9217 (mtp) cc_final: 0.8799 (mtp) REVERT: X 134 GLU cc_start: 0.8603 (pt0) cc_final: 0.8243 (pm20) REVERT: Y 38 GLN cc_start: 0.9212 (tt0) cc_final: 0.8984 (tt0) REVERT: Y 40 ASP cc_start: 0.8639 (t0) cc_final: 0.8393 (t70) REVERT: Y 87 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8792 (ttp80) REVERT: Y 177 GLU cc_start: 0.9025 (tp30) cc_final: 0.8816 (tp30) REVERT: Y 200 GLU cc_start: 0.8887 (pt0) cc_final: 0.8453 (pt0) REVERT: Z 131 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8158 (mmt) REVERT: Z 191 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.8072 (m110) REVERT: Z 194 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8302 (mp) REVERT: Z 244 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8370 (mmtt) REVERT: Z 280 GLU cc_start: 0.8229 (pt0) cc_final: 0.7836 (mp0) REVERT: Z 281 LYS cc_start: 0.8704 (mttm) cc_final: 0.8367 (mtmt) REVERT: a 201 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8581 (ttpm) REVERT: a 242 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8020 (mm-30) REVERT: a 295 GLU cc_start: 0.8482 (mp0) cc_final: 0.8052 (mp0) REVERT: a 337 ARG cc_start: 0.8748 (mtt-85) cc_final: 0.8491 (mmm160) REVERT: b 100 ASP cc_start: 0.8145 (t70) cc_final: 0.7878 (t70) REVERT: b 115 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7892 (tm-30) REVERT: b 179 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8630 (mpt180) outliers start: 295 outliers final: 153 residues processed: 1142 average time/residue: 1.7358 time to fit residues: 2434.4970 Evaluate side-chains 1133 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 933 time to evaluate : 5.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 402 LYS Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain J residue 12 MET Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 159 LEU Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 260 LEU Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain O residue 173 LYS Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 236 ASN Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 172 GLN Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain S residue 107 GLU Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 300 ASP Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 243 VAL Chi-restraints excluded: chain T residue 348 THR Chi-restraints excluded: chain T residue 365 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 182 SER Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 227 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 140 MET Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 252 MET Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain W residue 210 ASP Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain Y residue 12 ASP Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 87 ARG Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain Z residue 245 ASP Chi-restraints excluded: chain Z residue 249 GLU Chi-restraints excluded: chain a residue 154 ASN Chi-restraints excluded: chain a residue 201 LYS Chi-restraints excluded: chain a residue 219 SER Chi-restraints excluded: chain a residue 253 VAL Chi-restraints excluded: chain a residue 327 ASP Chi-restraints excluded: chain b residue 71 LYS Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 179 ARG Chi-restraints excluded: chain b residue 192 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 495 optimal weight: 3.9990 chunk 337 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 443 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 508 optimal weight: 0.9980 chunk 411 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 304 optimal weight: 3.9990 chunk 534 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 228 ASN B 100 ASN C 62 GLN E 191 HIS E 286 HIS I 247 GLN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 GLN L 222 GLN ** L 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN N 70 GLN O 228 ASN S 255 GLN T 195 ASN ** T 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 305 GLN V 241 GLN V 246 ASN ** W 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 229 GLN ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN a 130 GLN a 180 ASN b 62 GLN b 105 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 50122 Z= 0.231 Angle : 0.510 9.140 67810 Z= 0.271 Chirality : 0.042 0.168 7544 Planarity : 0.004 0.050 8790 Dihedral : 7.507 89.415 7159 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.72 % Favored : 98.19 % Rotamer: Outliers : 5.21 % Allowed : 21.19 % Favored : 73.60 % 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: 0.93 (0.10), residues: 6290 helix: 1.95 (0.11), residues: 2344 sheet: -0.09 (0.12), residues: 1602 loop : -0.13 (0.12), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 165 HIS 0.008 0.001 HIS R 187 PHE 0.017 0.001 PHE K 8 TYR 0.018 0.001 TYR K 128 ARG 0.005 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1269 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 996 time to evaluate : 6.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8334 (tm-30) REVERT: A 125 GLN cc_start: 0.8078 (mt0) cc_final: 0.7676 (mm-40) REVERT: A 161 TRP cc_start: 0.8717 (t60) cc_final: 0.8251 (t-100) REVERT: A 184 ARG cc_start: 0.7979 (tpp80) cc_final: 0.7436 (mmm160) REVERT: A 215 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8144 (mmmt) REVERT: A 217 LYS cc_start: 0.8627 (tttt) cc_final: 0.8049 (pttt) REVERT: B 3 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6052 (tt0) REVERT: B 16 LYS cc_start: 0.8606 (ptmt) cc_final: 0.8260 (ptmt) REVERT: B 118 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8161 (tt0) REVERT: B 181 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7556 (mt-10) REVERT: B 184 ASP cc_start: 0.7847 (t0) cc_final: 0.7583 (m-30) REVERT: B 210 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8440 (ptt90) REVERT: C 40 LYS cc_start: 0.8451 (mmtp) cc_final: 0.7901 (pttt) REVERT: C 196 LEU cc_start: 0.9018 (tp) cc_final: 0.8810 (tt) REVERT: C 237 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8217 (tppt) REVERT: C 265 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7241 (tpt-90) REVERT: D 52 LYS cc_start: 0.7994 (mttp) cc_final: 0.7551 (mppt) REVERT: D 57 ARG cc_start: 0.7783 (tmm160) cc_final: 0.7305 (ptt90) REVERT: D 61 LYS cc_start: 0.8828 (mptp) cc_final: 0.8529 (mmpt) REVERT: D 100 ASP cc_start: 0.8953 (m-30) cc_final: 0.8742 (m-30) REVERT: D 177 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7916 (mmtp) REVERT: D 180 MET cc_start: 0.8283 (mtt) cc_final: 0.7904 (mtm) REVERT: D 215 ARG cc_start: 0.8447 (ttp-170) cc_final: 0.8015 (mtp-110) REVERT: D 221 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7134 (tp30) REVERT: D 232 GLU cc_start: 0.7234 (tt0) cc_final: 0.6755 (mt-10) REVERT: E 140 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8721 (mm) REVERT: E 190 GLU cc_start: 0.8384 (tp30) cc_final: 0.8029 (tp30) REVERT: E 278 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7569 (mt0) REVERT: E 300 ASP cc_start: 0.7973 (m-30) cc_final: 0.7424 (m-30) REVERT: E 326 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8294 (mmtm) REVERT: E 342 MET cc_start: 0.6570 (ttm) cc_final: 0.6079 (ttm) REVERT: F 270 MET cc_start: 0.9023 (mmm) cc_final: 0.8660 (mmm) REVERT: F 402 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6805 (tptp) REVERT: G 13 ASP cc_start: 0.8631 (p0) cc_final: 0.8389 (p0) REVERT: G 44 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8103 (m-30) REVERT: G 51 GLU cc_start: 0.8173 (tt0) cc_final: 0.7929 (tm-30) REVERT: G 115 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8229 (mpt-90) REVERT: G 182 SER cc_start: 0.8515 (m) cc_final: 0.8310 (p) REVERT: H 139 LYS cc_start: 0.8738 (ttmm) cc_final: 0.8419 (ttpp) REVERT: H 143 MET cc_start: 0.8224 (ttp) cc_final: 0.8001 (tpp) REVERT: H 201 MET cc_start: 0.8940 (mtt) cc_final: 0.8611 (mtt) REVERT: H 279 MET cc_start: 0.8968 (mtm) cc_final: 0.8500 (mtp) REVERT: I 118 ARG cc_start: 0.8845 (ttm170) cc_final: 0.8588 (ttp-110) REVERT: I 225 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6887 (mtt) REVERT: I 226 TYR cc_start: 0.7125 (t80) cc_final: 0.6486 (t80) REVERT: I 229 GLN cc_start: 0.7623 (mm110) cc_final: 0.7088 (mm110) REVERT: I 230 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: J 4 MET cc_start: 0.9135 (mmm) cc_final: 0.8859 (mmt) REVERT: J 38 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8565 (mm-30) REVERT: J 79 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: J 97 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8148 (mt-10) REVERT: J 114 LYS cc_start: 0.8031 (tttt) cc_final: 0.7625 (mmtm) REVERT: J 134 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7583 (pp20) REVERT: K 1 MET cc_start: 0.7626 (mmm) cc_final: 0.7070 (mmm) REVERT: K 196 LYS cc_start: 0.8720 (ptmm) cc_final: 0.8490 (ptmm) REVERT: K 200 GLU cc_start: 0.8895 (pt0) cc_final: 0.8533 (pt0) REVERT: K 206 HIS cc_start: 0.8158 (p90) cc_final: 0.7943 (p90) REVERT: L 134 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8400 (mp) REVERT: L 155 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: L 191 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7841 (m110) REVERT: M 174 TYR cc_start: 0.8756 (m-10) cc_final: 0.8016 (m-10) REVERT: M 201 LYS cc_start: 0.8710 (mtpm) cc_final: 0.8437 (mtpp) REVERT: M 212 LYS cc_start: 0.9032 (tttm) cc_final: 0.8777 (ttpp) REVERT: M 226 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7203 (ptp-170) REVERT: M 257 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8663 (pt0) REVERT: M 281 ARG cc_start: 0.8526 (mtp85) cc_final: 0.8005 (mtp-110) REVERT: M 332 GLU cc_start: 0.8362 (pt0) cc_final: 0.8135 (pt0) REVERT: N 106 MET cc_start: 0.8791 (mpt) cc_final: 0.8103 (mpt) REVERT: N 151 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: N 179 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8618 (mtt-85) REVERT: N 183 LYS cc_start: 0.8951 (ttpt) cc_final: 0.8712 (tppp) REVERT: N 195 ARG cc_start: 0.8699 (mtp-110) cc_final: 0.8295 (mtp85) REVERT: N 203 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: O 7 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7263 (p0) REVERT: O 85 ARG cc_start: 0.8844 (tpt170) cc_final: 0.8588 (tpt170) REVERT: O 93 GLU cc_start: 0.8159 (tt0) cc_final: 0.7607 (tm-30) REVERT: O 97 ASP cc_start: 0.8294 (m-30) cc_final: 0.7827 (m-30) REVERT: O 115 MET cc_start: 0.9220 (mmm) cc_final: 0.8943 (mmp) REVERT: O 125 GLN cc_start: 0.8324 (mt0) cc_final: 0.8097 (tt0) REVERT: O 173 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7872 (mmpt) REVERT: O 190 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8387 (mp) REVERT: P 16 LYS cc_start: 0.8815 (ptmt) cc_final: 0.8030 (mmtm) REVERT: P 85 ILE cc_start: 0.9207 (mt) cc_final: 0.8926 (mt) REVERT: P 100 ASN cc_start: 0.8656 (t0) cc_final: 0.8415 (t0) REVERT: P 202 THR cc_start: 0.8956 (p) cc_final: 0.8611 (t) REVERT: P 225 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.7410 (mtt180) REVERT: Q 29 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: Q 53 HIS cc_start: 0.8731 (t-90) cc_final: 0.8307 (t-90) REVERT: Q 193 ASP cc_start: 0.8505 (t0) cc_final: 0.8216 (m-30) REVERT: Q 204 LYS cc_start: 0.8637 (tttt) cc_final: 0.8202 (tptp) REVERT: Q 266 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6642 (tm-30) REVERT: R 23 GLN cc_start: 0.8207 (mt0) cc_final: 0.7902 (mm-40) REVERT: R 49 SER cc_start: 0.6450 (t) cc_final: 0.5982 (p) REVERT: R 54 GLN cc_start: 0.8286 (pt0) cc_final: 0.7607 (mm110) REVERT: R 174 LYS cc_start: 0.7961 (mmtp) cc_final: 0.7637 (mtmm) REVERT: R 213 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7875 (mp0) REVERT: S 118 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: S 249 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8397 (mmmt) REVERT: S 313 GLU cc_start: 0.8703 (mp0) cc_final: 0.8416 (mp0) REVERT: S 336 LYS cc_start: 0.8029 (tttt) cc_final: 0.7581 (tppp) REVERT: T 190 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7705 (m-40) REVERT: T 279 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7905 (mm-30) REVERT: T 343 HIS cc_start: 0.7211 (m90) cc_final: 0.6860 (m-70) REVERT: T 347 CYS cc_start: 0.8755 (m) cc_final: 0.8379 (m) REVERT: T 395 ARG cc_start: 0.7148 (mtm-85) cc_final: 0.6720 (mtm-85) REVERT: T 404 ARG cc_start: 0.5572 (OUTLIER) cc_final: 0.5143 (ppt170) REVERT: U 94 GLN cc_start: 0.8596 (tt0) cc_final: 0.8282 (tm-30) REVERT: U 114 ASN cc_start: 0.8929 (m-40) cc_final: 0.8545 (m110) REVERT: U 203 LYS cc_start: 0.7936 (mttt) cc_final: 0.7451 (mtmm) REVERT: V 140 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8444 (mtp) REVERT: V 143 MET cc_start: 0.8439 (ttp) cc_final: 0.8101 (mmp) REVERT: V 201 MET cc_start: 0.8822 (mtt) cc_final: 0.8562 (mtm) REVERT: V 273 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8074 (tppt) REVERT: W 61 ARG cc_start: 0.7698 (mtp85) cc_final: 0.7386 (mmt180) REVERT: W 82 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: W 106 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8955 (tt) REVERT: W 119 TYR cc_start: 0.8994 (m-80) cc_final: 0.8760 (m-80) REVERT: W 225 MET cc_start: 0.7278 (mtp) cc_final: 0.7075 (mtm) REVERT: X 6 TYR cc_start: 0.9053 (t80) cc_final: 0.8771 (t80) REVERT: X 17 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8585 (ttmm) REVERT: X 38 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8566 (mm-30) REVERT: X 79 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8681 (mt-10) REVERT: X 94 MET cc_start: 0.9209 (mtp) cc_final: 0.8714 (mtp) REVERT: X 134 GLU cc_start: 0.8572 (pt0) cc_final: 0.8289 (pm20) REVERT: X 183 TYR cc_start: 0.8960 (m-80) cc_final: 0.8374 (m-80) REVERT: Y 38 GLN cc_start: 0.9173 (tt0) cc_final: 0.8935 (tt0) REVERT: Y 40 ASP cc_start: 0.8626 (t0) cc_final: 0.8380 (t70) REVERT: Y 87 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8797 (ttp80) REVERT: Y 200 GLU cc_start: 0.8883 (pt0) cc_final: 0.8445 (pt0) REVERT: Z 131 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8185 (mmt) REVERT: Z 244 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8389 (mmtt) REVERT: Z 280 GLU cc_start: 0.8224 (pt0) cc_final: 0.7809 (mp0) REVERT: Z 281 LYS cc_start: 0.8707 (mttm) cc_final: 0.8367 (mtmt) REVERT: a 201 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8592 (ttpm) REVERT: a 242 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8004 (mm-30) REVERT: a 295 GLU cc_start: 0.8373 (mp0) cc_final: 0.7889 (mp0) REVERT: b 100 ASP cc_start: 0.8155 (t70) cc_final: 0.7908 (t70) REVERT: b 106 MET cc_start: 0.8872 (mtt) cc_final: 0.8311 (mtt) REVERT: b 179 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8633 (mpt180) outliers start: 273 outliers final: 137 residues processed: 1156 average time/residue: 1.7585 time to fit residues: 2510.5661 Evaluate side-chains 1124 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 947 time to evaluate : 5.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 402 LYS Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain J residue 12 MET Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 159 LEU Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 260 LEU Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain O residue 173 LYS Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 172 GLN Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 184 ASP Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 300 ASP Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 348 THR Chi-restraints excluded: chain T residue 365 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 182 SER Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 188 GLU Chi-restraints excluded: chain U residue 227 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 140 MET Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 252 MET Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain W residue 210 ASP Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain Y residue 12 ASP Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 87 ARG Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 152 GLN Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain Z residue 249 GLU Chi-restraints excluded: chain a residue 201 LYS Chi-restraints excluded: chain a residue 253 VAL Chi-restraints excluded: chain a residue 293 THR Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 179 ARG Chi-restraints excluded: chain b residue 192 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 200 optimal weight: 0.6980 chunk 536 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 349 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 596 optimal weight: 0.9980 chunk 494 optimal weight: 0.9990 chunk 275 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 312 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 228 ASN B 100 ASN B 205 ASN C 62 GLN D 187 HIS F 225 GLN F 371 ASN I 247 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 GLN L 123 GLN L 222 GLN L 291 GLN M 130 GLN N 66 ASN N 70 GLN O 228 ASN P 107 GLN P 205 ASN R 223 GLN S 191 HIS S 255 GLN T 195 ASN ** T 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 305 GLN V 241 GLN V 246 ASN W 229 GLN ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN a 130 GLN a 180 ASN b 62 GLN b 105 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 50122 Z= 0.173 Angle : 0.485 8.647 67810 Z= 0.258 Chirality : 0.041 0.165 7544 Planarity : 0.004 0.048 8790 Dihedral : 7.139 89.975 7140 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.92 % Favored : 97.98 % Rotamer: Outliers : 4.81 % Allowed : 21.86 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.10), residues: 6290 helix: 2.13 (0.11), residues: 2346 sheet: 0.00 (0.12), residues: 1584 loop : -0.10 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 154 HIS 0.007 0.001 HIS R 187 PHE 0.016 0.001 PHE K 8 TYR 0.017 0.001 TYR J 96 ARG 0.006 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 986 time to evaluate : 5.505 Fit side-chains revert: symmetry clash REVERT: A 14 SER cc_start: 0.9335 (p) cc_final: 0.9124 (t) REVERT: A 125 GLN cc_start: 0.8033 (mt0) cc_final: 0.7651 (mm-40) REVERT: A 161 TRP cc_start: 0.8651 (t60) cc_final: 0.8133 (t-100) REVERT: A 184 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7448 (mmm160) REVERT: A 215 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8150 (mmmt) REVERT: A 217 LYS cc_start: 0.8611 (tttt) cc_final: 0.8039 (pttt) REVERT: B 16 LYS cc_start: 0.8576 (ptmt) cc_final: 0.8248 (ptmt) REVERT: B 118 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8142 (tt0) REVERT: B 184 ASP cc_start: 0.7791 (t0) cc_final: 0.7568 (m-30) REVERT: B 210 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8390 (ptt90) REVERT: C 40 LYS cc_start: 0.8461 (mmtp) cc_final: 0.7858 (pttt) REVERT: C 119 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8516 (tt) REVERT: C 196 LEU cc_start: 0.9011 (tp) cc_final: 0.8786 (tt) REVERT: C 237 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8224 (tppt) REVERT: C 265 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7186 (tpt-90) REVERT: D 52 LYS cc_start: 0.7918 (mttp) cc_final: 0.7519 (mppt) REVERT: D 57 ARG cc_start: 0.7398 (tmm160) cc_final: 0.6984 (ptt90) REVERT: D 61 LYS cc_start: 0.8802 (mptp) cc_final: 0.8498 (mmpt) REVERT: D 177 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7910 (mmtp) REVERT: D 180 MET cc_start: 0.8261 (mtt) cc_final: 0.7892 (mtm) REVERT: D 215 ARG cc_start: 0.8447 (ttp-170) cc_final: 0.8001 (mtp-110) REVERT: D 221 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7247 (tp30) REVERT: D 232 GLU cc_start: 0.7300 (tt0) cc_final: 0.6860 (mt-10) REVERT: E 140 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8694 (mm) REVERT: E 190 GLU cc_start: 0.8375 (tp30) cc_final: 0.8098 (tp30) REVERT: E 278 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7519 (mt0) REVERT: E 300 ASP cc_start: 0.7986 (m-30) cc_final: 0.7439 (m-30) REVERT: E 326 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8345 (mmtm) REVERT: E 342 MET cc_start: 0.6437 (ttm) cc_final: 0.5952 (ttm) REVERT: F 270 MET cc_start: 0.8961 (mmm) cc_final: 0.8573 (mmm) REVERT: F 402 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6650 (tptp) REVERT: G 13 ASP cc_start: 0.8675 (p0) cc_final: 0.8462 (p0) REVERT: G 44 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8071 (m-30) REVERT: G 51 GLU cc_start: 0.8147 (tt0) cc_final: 0.7896 (tm-30) REVERT: G 115 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8265 (mpt-90) REVERT: H 139 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8391 (ttpp) REVERT: H 143 MET cc_start: 0.8204 (ttp) cc_final: 0.7995 (tpp) REVERT: H 201 MET cc_start: 0.8956 (mtt) cc_final: 0.8617 (mtm) REVERT: H 279 MET cc_start: 0.8919 (mtm) cc_final: 0.8441 (mtp) REVERT: I 118 ARG cc_start: 0.8820 (ttm170) cc_final: 0.8554 (ttp-110) REVERT: I 225 MET cc_start: 0.7125 (mtp) cc_final: 0.6722 (mtt) REVERT: I 226 TYR cc_start: 0.7168 (t80) cc_final: 0.6520 (t80) REVERT: J 4 MET cc_start: 0.9120 (mmm) cc_final: 0.8882 (mmt) REVERT: J 38 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8540 (mm-30) REVERT: J 75 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8565 (mmtt) REVERT: J 79 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8284 (mt-10) REVERT: J 97 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8192 (mt-10) REVERT: J 114 LYS cc_start: 0.8056 (tttt) cc_final: 0.7679 (mmtm) REVERT: K 1 MET cc_start: 0.7590 (mmm) cc_final: 0.7096 (mmm) REVERT: K 22 ASN cc_start: 0.8884 (t0) cc_final: 0.8640 (t0) REVERT: K 181 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8926 (mmt-90) REVERT: K 200 GLU cc_start: 0.8875 (pt0) cc_final: 0.8514 (pt0) REVERT: K 206 HIS cc_start: 0.8149 (p90) cc_final: 0.7946 (p90) REVERT: L 134 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8361 (mp) REVERT: L 155 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: L 191 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7895 (m110) REVERT: M 174 TYR cc_start: 0.8747 (m-10) cc_final: 0.7897 (m-10) REVERT: M 201 LYS cc_start: 0.8721 (mtpm) cc_final: 0.8493 (mtpt) REVERT: M 212 LYS cc_start: 0.9010 (tttm) cc_final: 0.8722 (ttpp) REVERT: M 226 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7214 (ptp-170) REVERT: M 296 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8603 (mt-10) REVERT: M 332 GLU cc_start: 0.8318 (pt0) cc_final: 0.8102 (pt0) REVERT: N 34 ASN cc_start: 0.9299 (p0) cc_final: 0.9078 (p0) REVERT: N 69 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8203 (mtt90) REVERT: N 77 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8213 (t0) REVERT: N 106 MET cc_start: 0.8793 (mpt) cc_final: 0.8079 (mpt) REVERT: N 179 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8545 (mtt90) REVERT: N 183 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8558 (tppt) REVERT: N 195 ARG cc_start: 0.8701 (mtp-110) cc_final: 0.8278 (mtp85) REVERT: N 203 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: O 6 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7238 (t80) REVERT: O 7 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7187 (p0) REVERT: O 93 GLU cc_start: 0.8125 (tt0) cc_final: 0.7582 (tm-30) REVERT: O 97 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: O 115 MET cc_start: 0.9204 (mmm) cc_final: 0.8922 (mmp) REVERT: O 125 GLN cc_start: 0.8307 (mt0) cc_final: 0.8021 (mm-40) REVERT: O 173 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7812 (mmpt) REVERT: O 190 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8347 (mp) REVERT: O 236 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8215 (m110) REVERT: P 16 LYS cc_start: 0.8711 (ptmt) cc_final: 0.8031 (mmtm) REVERT: P 85 ILE cc_start: 0.9207 (mt) cc_final: 0.8908 (mt) REVERT: P 100 ASN cc_start: 0.8637 (t0) cc_final: 0.8377 (t0) REVERT: P 202 THR cc_start: 0.8951 (p) cc_final: 0.8601 (t) REVERT: Q 29 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7987 (mp10) REVERT: Q 53 HIS cc_start: 0.8724 (t-90) cc_final: 0.8274 (t-90) REVERT: Q 193 ASP cc_start: 0.8492 (t0) cc_final: 0.8233 (m-30) REVERT: Q 204 LYS cc_start: 0.8629 (tttt) cc_final: 0.8209 (tptp) REVERT: Q 266 GLU cc_start: 0.6874 (tm-30) cc_final: 0.6637 (tm-30) REVERT: R 23 GLN cc_start: 0.8187 (mt0) cc_final: 0.7878 (mm-40) REVERT: R 49 SER cc_start: 0.6346 (t) cc_final: 0.5900 (p) REVERT: R 54 GLN cc_start: 0.8329 (pt0) cc_final: 0.7656 (mm110) REVERT: R 174 LYS cc_start: 0.7928 (mmtp) cc_final: 0.7629 (mtmm) REVERT: R 210 GLN cc_start: 0.9377 (OUTLIER) cc_final: 0.9110 (mt0) REVERT: R 213 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7810 (mp0) REVERT: R 215 ARG cc_start: 0.8476 (tmm-80) cc_final: 0.8226 (tmt90) REVERT: S 118 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: S 249 LYS cc_start: 0.8746 (mmtm) cc_final: 0.8384 (mmmt) REVERT: S 313 GLU cc_start: 0.8727 (mp0) cc_final: 0.8458 (mp0) REVERT: S 336 LYS cc_start: 0.7985 (tttt) cc_final: 0.7519 (tppp) REVERT: T 279 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7776 (mm-30) REVERT: T 343 HIS cc_start: 0.7122 (m90) cc_final: 0.6748 (m-70) REVERT: T 347 CYS cc_start: 0.8678 (m) cc_final: 0.8301 (m) REVERT: T 395 ARG cc_start: 0.7044 (mtm-85) cc_final: 0.6610 (mtm-85) REVERT: T 404 ARG cc_start: 0.5649 (OUTLIER) cc_final: 0.5139 (ppt170) REVERT: U 94 GLN cc_start: 0.8616 (tt0) cc_final: 0.8299 (tm-30) REVERT: U 188 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8340 (pt0) REVERT: V 140 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8452 (mtp) REVERT: V 143 MET cc_start: 0.8416 (ttp) cc_final: 0.8083 (mmp) REVERT: V 201 MET cc_start: 0.8817 (mtt) cc_final: 0.8589 (mtm) REVERT: V 273 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8036 (tppt) REVERT: W 61 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7487 (mmt90) REVERT: W 82 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: W 225 MET cc_start: 0.7253 (mtp) cc_final: 0.6830 (mtt) REVERT: X 6 TYR cc_start: 0.9027 (t80) cc_final: 0.8748 (t80) REVERT: X 17 LYS cc_start: 0.8843 (ttpt) cc_final: 0.8546 (ttmm) REVERT: X 38 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8549 (mm-30) REVERT: X 79 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8666 (mt-10) REVERT: X 134 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8200 (pm20) REVERT: X 183 TYR cc_start: 0.8897 (m-80) cc_final: 0.8309 (m-80) REVERT: Y 38 GLN cc_start: 0.9124 (tt0) cc_final: 0.8908 (tt0) REVERT: Y 40 ASP cc_start: 0.8620 (t0) cc_final: 0.8360 (t70) REVERT: Y 87 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8751 (ttp80) REVERT: Y 200 GLU cc_start: 0.8870 (pt0) cc_final: 0.8420 (pt0) REVERT: Z 131 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8145 (mmt) REVERT: Z 244 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8318 (mmtt) REVERT: Z 280 GLU cc_start: 0.8216 (pt0) cc_final: 0.7803 (mp0) REVERT: Z 281 LYS cc_start: 0.8700 (mttm) cc_final: 0.8367 (mtmt) REVERT: a 242 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8098 (mm-30) REVERT: b 100 ASP cc_start: 0.8136 (t70) cc_final: 0.7915 (t70) REVERT: b 106 MET cc_start: 0.8881 (mtt) cc_final: 0.8354 (mtt) outliers start: 252 outliers final: 120 residues processed: 1129 average time/residue: 1.6734 time to fit residues: 2338.4511 Evaluate side-chains 1107 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 946 time to evaluate : 5.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 402 LYS Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain J residue 12 MET Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 260 LEU Chi-restraints excluded: chain M residue 317 ASP Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 6 PHE Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 97 ASP Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain O residue 173 LYS Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 236 ASN Chi-restraints excluded: chain P residue 20 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 172 GLN Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 237 LYS Chi-restraints excluded: chain Q residue 268 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain S residue 107 GLU Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 255 GLN Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 348 THR Chi-restraints excluded: chain T residue 365 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 182 SER Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 188 GLU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 140 MET Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 246 ASN Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 210 ASP Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain X residue 47 ASP Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 87 ARG Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 196 MET Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain a residue 154 ASN Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain a residue 293 THR Chi-restraints excluded: chain b residue 28 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 574 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 339 optimal weight: 0.5980 chunk 435 optimal weight: 3.9990 chunk 337 optimal weight: 7.9990 chunk 501 optimal weight: 0.7980 chunk 332 optimal weight: 4.9990 chunk 593 optimal weight: 4.9990 chunk 371 optimal weight: 0.7980 chunk 361 optimal weight: 4.9990 chunk 274 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 100 ASN D 187 HIS F 206 ASN I 247 GLN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 197 ASN L 123 GLN L 222 GLN ** L 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN N 70 GLN O 228 ASN P 93 GLN P 205 ASN R 223 GLN T 195 ASN T 271 ASN T 305 GLN V 241 GLN W 229 GLN ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN a 180 ASN b 105 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 50122 Z= 0.267 Angle : 0.517 8.798 67810 Z= 0.274 Chirality : 0.043 0.167 7544 Planarity : 0.004 0.047 8790 Dihedral : 6.885 89.928 7107 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.88 % Favored : 98.04 % Rotamer: Outliers : 4.87 % Allowed : 22.03 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.10), residues: 6290 helix: 2.06 (0.11), residues: 2352 sheet: 0.02 (0.12), residues: 1592 loop : -0.05 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 165 HIS 0.008 0.001 HIS R 187 PHE 0.017 0.002 PHE K 8 TYR 0.022 0.001 TYR J 96 ARG 0.005 0.000 ARG Z 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 960 time to evaluate : 5.798 Fit side-chains revert: symmetry clash REVERT: A 14 SER cc_start: 0.9349 (p) cc_final: 0.9145 (t) REVERT: A 125 GLN cc_start: 0.8067 (mt0) cc_final: 0.7679 (mm-40) REVERT: A 161 TRP cc_start: 0.8673 (t60) cc_final: 0.8160 (t-100) REVERT: A 184 ARG cc_start: 0.8012 (tpp80) cc_final: 0.7460 (mmm160) REVERT: A 215 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8195 (mmmt) REVERT: A 217 LYS cc_start: 0.8594 (tttt) cc_final: 0.7986 (pttp) REVERT: B 3 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: B 16 LYS cc_start: 0.8609 (ptmt) cc_final: 0.8278 (ptmt) REVERT: B 118 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8167 (tt0) REVERT: B 210 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8468 (ptt90) REVERT: C 40 LYS cc_start: 0.8520 (mmtp) cc_final: 0.7929 (pttt) REVERT: C 119 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8493 (tt) REVERT: C 196 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8811 (tt) REVERT: C 237 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8398 (tptp) REVERT: C 265 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7199 (tpt-90) REVERT: D 52 LYS cc_start: 0.7937 (mttp) cc_final: 0.7543 (mppt) REVERT: D 57 ARG cc_start: 0.7582 (tmm160) cc_final: 0.7114 (ptt90) REVERT: D 177 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7887 (mmtp) REVERT: D 180 MET cc_start: 0.8271 (mtt) cc_final: 0.7895 (mtm) REVERT: D 215 ARG cc_start: 0.8447 (ttp-170) cc_final: 0.7994 (mtp-110) REVERT: D 221 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7058 (tp30) REVERT: D 232 GLU cc_start: 0.7244 (tt0) cc_final: 0.6786 (mt-10) REVERT: E 107 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.5973 (mp0) REVERT: E 140 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8711 (mm) REVERT: E 190 GLU cc_start: 0.8413 (tp30) cc_final: 0.8171 (tp30) REVERT: E 278 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7536 (mt0) REVERT: E 300 ASP cc_start: 0.7994 (m-30) cc_final: 0.7460 (m-30) REVERT: E 326 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8393 (mmtm) REVERT: E 342 MET cc_start: 0.6432 (ttm) cc_final: 0.5950 (ttm) REVERT: F 270 MET cc_start: 0.9048 (mmm) cc_final: 0.8646 (mmm) REVERT: F 402 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6763 (tptp) REVERT: G 13 ASP cc_start: 0.8641 (p0) cc_final: 0.8406 (p0) REVERT: G 44 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8112 (m-30) REVERT: G 51 GLU cc_start: 0.8165 (tt0) cc_final: 0.7911 (tm-30) REVERT: G 115 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8212 (mmt90) REVERT: H 123 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8617 (p0) REVERT: H 139 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8435 (ttpp) REVERT: H 143 MET cc_start: 0.8230 (ttp) cc_final: 0.7998 (tpp) REVERT: H 201 MET cc_start: 0.8962 (mtt) cc_final: 0.8586 (mtt) REVERT: I 118 ARG cc_start: 0.8829 (ttm170) cc_final: 0.8597 (ttp-110) REVERT: I 225 MET cc_start: 0.7106 (mtp) cc_final: 0.6715 (mtt) REVERT: I 226 TYR cc_start: 0.7117 (t80) cc_final: 0.6467 (t80) REVERT: I 230 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7775 (mm-30) REVERT: J 4 MET cc_start: 0.9124 (mmm) cc_final: 0.8847 (mmt) REVERT: J 38 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8566 (mm-30) REVERT: J 97 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8207 (mt-10) REVERT: J 114 LYS cc_start: 0.8081 (tttt) cc_final: 0.7690 (mmtm) REVERT: K 22 ASN cc_start: 0.8909 (t0) cc_final: 0.8629 (t0) REVERT: K 196 LYS cc_start: 0.8658 (ptmm) cc_final: 0.8452 (ptmm) REVERT: K 200 GLU cc_start: 0.8876 (pt0) cc_final: 0.8520 (pt0) REVERT: K 206 HIS cc_start: 0.8159 (p90) cc_final: 0.7949 (p90) REVERT: L 155 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: L 191 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7925 (m110) REVERT: M 174 TYR cc_start: 0.8753 (m-10) cc_final: 0.7999 (m-10) REVERT: M 201 LYS cc_start: 0.8732 (mtpm) cc_final: 0.8468 (mtpp) REVERT: M 212 LYS cc_start: 0.9037 (tttm) cc_final: 0.8778 (ttpp) REVERT: M 226 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7245 (ptp-170) REVERT: M 257 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8684 (pt0) REVERT: M 281 ARG cc_start: 0.8469 (mtp85) cc_final: 0.7988 (mtp-110) REVERT: M 296 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8611 (mt-10) REVERT: M 332 GLU cc_start: 0.8343 (pt0) cc_final: 0.8114 (pt0) REVERT: N 69 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8182 (mtt90) REVERT: N 106 MET cc_start: 0.8789 (mpt) cc_final: 0.8077 (mpt) REVERT: N 179 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8608 (mtt-85) REVERT: N 183 LYS cc_start: 0.8946 (ttpt) cc_final: 0.8729 (tppp) REVERT: N 195 ARG cc_start: 0.8690 (mtp-110) cc_final: 0.8256 (mtp85) REVERT: N 203 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: O 6 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.7293 (t80) REVERT: O 7 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7273 (p0) REVERT: O 93 GLU cc_start: 0.8157 (tt0) cc_final: 0.7640 (tm-30) REVERT: O 97 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: O 115 MET cc_start: 0.9239 (mmm) cc_final: 0.8980 (mmp) REVERT: O 125 GLN cc_start: 0.8338 (mt0) cc_final: 0.8111 (tt0) REVERT: O 173 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7839 (mmpt) REVERT: O 190 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8372 (mp) REVERT: O 236 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8165 (m110) REVERT: P 16 LYS cc_start: 0.8820 (ptmt) cc_final: 0.8085 (mmtm) REVERT: P 85 ILE cc_start: 0.9228 (mt) cc_final: 0.8961 (mt) REVERT: P 100 ASN cc_start: 0.8638 (t0) cc_final: 0.8372 (t0) REVERT: P 202 THR cc_start: 0.8902 (p) cc_final: 0.8551 (t) REVERT: Q 29 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8275 (mp10) REVERT: Q 53 HIS cc_start: 0.8735 (t-90) cc_final: 0.8269 (t-90) REVERT: Q 193 ASP cc_start: 0.8469 (t0) cc_final: 0.8189 (m-30) REVERT: Q 204 LYS cc_start: 0.8595 (tttt) cc_final: 0.8235 (tptp) REVERT: Q 206 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8299 (mtp) REVERT: Q 266 GLU cc_start: 0.6853 (tm-30) cc_final: 0.6629 (tm-30) REVERT: R 23 GLN cc_start: 0.8210 (mt0) cc_final: 0.7902 (mm-40) REVERT: R 49 SER cc_start: 0.6462 (t) cc_final: 0.6011 (p) REVERT: R 54 GLN cc_start: 0.8322 (pt0) cc_final: 0.7659 (mm110) REVERT: R 174 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7653 (mtmm) REVERT: R 210 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.9086 (mt0) REVERT: R 213 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7804 (mp0) REVERT: R 215 ARG cc_start: 0.8501 (tmm-80) cc_final: 0.8246 (tmt90) REVERT: R 219 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: S 118 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: S 249 LYS cc_start: 0.8758 (mmtm) cc_final: 0.8397 (mmmt) REVERT: S 313 GLU cc_start: 0.8764 (mp0) cc_final: 0.8491 (mp0) REVERT: S 336 LYS cc_start: 0.7997 (tttt) cc_final: 0.7549 (tppp) REVERT: T 190 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7721 (m-40) REVERT: T 279 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7835 (mm-30) REVERT: T 343 HIS cc_start: 0.7141 (m90) cc_final: 0.6773 (m-70) REVERT: T 347 CYS cc_start: 0.8709 (m) cc_final: 0.8305 (m) REVERT: T 395 ARG cc_start: 0.7052 (mtm-85) cc_final: 0.6627 (mtm-85) REVERT: T 404 ARG cc_start: 0.5772 (OUTLIER) cc_final: 0.5317 (ppt170) REVERT: U 94 GLN cc_start: 0.8570 (tt0) cc_final: 0.8241 (tm-30) REVERT: U 185 THR cc_start: 0.8940 (p) cc_final: 0.8669 (p) REVERT: U 188 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8326 (pt0) REVERT: V 140 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8423 (mtp) REVERT: V 143 MET cc_start: 0.8424 (ttp) cc_final: 0.8090 (mmp) REVERT: V 201 MET cc_start: 0.8841 (mtt) cc_final: 0.8593 (mtm) REVERT: V 273 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8075 (tppt) REVERT: W 61 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7488 (mmt90) REVERT: W 82 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8499 (tt0) REVERT: W 87 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8511 (ptm) REVERT: W 119 TYR cc_start: 0.9022 (m-80) cc_final: 0.8817 (m-80) REVERT: W 225 MET cc_start: 0.7219 (mtp) cc_final: 0.6756 (mtt) REVERT: X 6 TYR cc_start: 0.9044 (t80) cc_final: 0.8784 (t80) REVERT: X 38 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8568 (mm-30) REVERT: X 79 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8689 (mt-10) REVERT: X 134 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8251 (pm20) REVERT: X 162 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8298 (pt0) REVERT: X 183 TYR cc_start: 0.8963 (m-80) cc_final: 0.8445 (m-80) REVERT: Y 38 GLN cc_start: 0.9101 (tt0) cc_final: 0.8897 (tt0) REVERT: Y 40 ASP cc_start: 0.8632 (t0) cc_final: 0.8380 (t70) REVERT: Y 200 GLU cc_start: 0.8843 (pt0) cc_final: 0.8426 (pt0) REVERT: Z 131 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8122 (mmt) REVERT: Z 244 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8352 (mmtt) REVERT: Z 280 GLU cc_start: 0.8231 (pt0) cc_final: 0.7818 (mp0) REVERT: Z 281 LYS cc_start: 0.8706 (mttm) cc_final: 0.8374 (mtmt) REVERT: a 242 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8010 (mm-30) REVERT: b 100 ASP cc_start: 0.8154 (t70) cc_final: 0.7923 (t70) REVERT: b 106 MET cc_start: 0.8907 (mtt) cc_final: 0.8403 (mtt) REVERT: b 112 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6866 (ttt180) REVERT: b 115 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7547 (tm-30) REVERT: b 179 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8284 (mpt180) outliers start: 255 outliers final: 150 residues processed: 1110 average time/residue: 1.7097 time to fit residues: 2336.3381 Evaluate side-chains 1128 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 932 time to evaluate : 5.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 402 LYS Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain J residue 12 MET Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 201 LYS Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain L residue 245 ASP Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 260 LEU Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain M residue 338 LYS Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 6 PHE Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 97 ASP Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain O residue 173 LYS Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 236 ASN Chi-restraints excluded: chain P residue 47 LYS Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 180 MET Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 172 GLN Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 206 MET Chi-restraints excluded: chain Q residue 237 LYS Chi-restraints excluded: chain Q residue 268 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain S residue 107 GLU Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 184 ASP Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 348 THR Chi-restraints excluded: chain T residue 365 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 182 SER Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 188 GLU Chi-restraints excluded: chain U residue 227 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 140 MET Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 241 GLN Chi-restraints excluded: chain V residue 246 ASN Chi-restraints excluded: chain V residue 252 MET Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 210 ASP Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain Y residue 12 ASP Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 152 GLN Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain Z residue 291 GLN Chi-restraints excluded: chain a residue 154 ASN Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain a residue 219 SER Chi-restraints excluded: chain a residue 293 THR Chi-restraints excluded: chain a residue 327 ASP Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 112 ARG Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 179 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 367 optimal weight: 0.8980 chunk 237 optimal weight: 8.9990 chunk 354 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 377 optimal weight: 0.7980 chunk 404 optimal weight: 4.9990 chunk 293 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 466 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 100 ASN C 62 GLN D 54 GLN D 97 ASN D 187 HIS G 147 GLN I 247 GLN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 GLN L 222 GLN L 291 GLN N 70 GLN O 228 ASN P 205 ASN Q 186 HIS R 223 GLN S 255 GLN T 195 ASN V 246 ASN W 229 GLN ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN a 130 GLN a 180 ASN b 62 GLN b 105 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 50122 Z= 0.209 Angle : 0.503 8.624 67810 Z= 0.266 Chirality : 0.042 0.167 7544 Planarity : 0.004 0.047 8790 Dihedral : 6.712 89.926 7104 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.89 % Favored : 98.04 % Rotamer: Outliers : 4.51 % Allowed : 22.51 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.10), residues: 6290 helix: 2.14 (0.11), residues: 2344 sheet: 0.04 (0.12), residues: 1576 loop : -0.03 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 165 HIS 0.007 0.001 HIS R 187 PHE 0.017 0.001 PHE K 8 TYR 0.024 0.001 TYR J 96 ARG 0.006 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1188 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 952 time to evaluate : 5.703 Fit side-chains revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8032 (mt0) cc_final: 0.7653 (mm-40) REVERT: A 161 TRP cc_start: 0.8667 (t60) cc_final: 0.8150 (t-100) REVERT: A 184 ARG cc_start: 0.8001 (tpp80) cc_final: 0.7461 (mmm160) REVERT: A 215 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8087 (mmmt) REVERT: A 217 LYS cc_start: 0.8577 (tttt) cc_final: 0.7976 (pttp) REVERT: B 3 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6968 (tt0) REVERT: B 16 LYS cc_start: 0.8602 (ptmt) cc_final: 0.8218 (ptmt) REVERT: B 21 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8374 (mt-10) REVERT: B 118 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8154 (tt0) REVERT: B 210 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8449 (ptt90) REVERT: C 40 LYS cc_start: 0.8517 (mmtp) cc_final: 0.7927 (pttt) REVERT: C 119 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8524 (tt) REVERT: C 196 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8802 (tt) REVERT: C 237 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8278 (tppt) REVERT: C 265 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7251 (tpt-90) REVERT: D 52 LYS cc_start: 0.7942 (mttp) cc_final: 0.7529 (mppt) REVERT: D 57 ARG cc_start: 0.7494 (tmm160) cc_final: 0.6995 (ptt90) REVERT: D 138 GLU cc_start: 0.8607 (tp30) cc_final: 0.8386 (mm-30) REVERT: D 177 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7899 (mmtp) REVERT: D 180 MET cc_start: 0.8226 (mtt) cc_final: 0.7849 (mtm) REVERT: D 215 ARG cc_start: 0.8433 (ttp-170) cc_final: 0.7985 (mtp-110) REVERT: D 221 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7204 (tp30) REVERT: D 232 GLU cc_start: 0.7246 (tt0) cc_final: 0.6812 (mt-10) REVERT: E 107 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.5994 (mp0) REVERT: E 140 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8717 (mm) REVERT: E 190 GLU cc_start: 0.8376 (tp30) cc_final: 0.8147 (tp30) REVERT: E 278 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7510 (mt0) REVERT: E 300 ASP cc_start: 0.7977 (m-30) cc_final: 0.7433 (m-30) REVERT: E 342 MET cc_start: 0.6605 (ttm) cc_final: 0.6099 (ttm) REVERT: F 270 MET cc_start: 0.8997 (mmm) cc_final: 0.8618 (mmm) REVERT: F 402 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6771 (tptp) REVERT: G 13 ASP cc_start: 0.8642 (p0) cc_final: 0.8402 (p0) REVERT: G 44 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: G 51 GLU cc_start: 0.8148 (tt0) cc_final: 0.7874 (tm-30) REVERT: G 115 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8222 (mmt90) REVERT: H 123 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8589 (p0) REVERT: H 139 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8406 (ttpp) REVERT: H 143 MET cc_start: 0.8218 (ttp) cc_final: 0.7999 (tpp) REVERT: H 201 MET cc_start: 0.8962 (mtt) cc_final: 0.8593 (mtm) REVERT: I 118 ARG cc_start: 0.8830 (ttm170) cc_final: 0.8588 (ttp-110) REVERT: I 225 MET cc_start: 0.7097 (mtp) cc_final: 0.6732 (mtt) REVERT: I 226 TYR cc_start: 0.7180 (t80) cc_final: 0.6523 (t80) REVERT: I 230 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7826 (mm-30) REVERT: J 4 MET cc_start: 0.9121 (mmm) cc_final: 0.8877 (mmt) REVERT: J 38 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8549 (mm-30) REVERT: J 75 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8539 (mmtt) REVERT: J 97 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8176 (mt-10) REVERT: J 114 LYS cc_start: 0.8040 (tttt) cc_final: 0.7670 (mmtm) REVERT: K 11 LYS cc_start: 0.9099 (tmmt) cc_final: 0.8887 (tttm) REVERT: K 22 ASN cc_start: 0.8884 (t0) cc_final: 0.8593 (t0) REVERT: K 181 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8130 (mpt180) REVERT: K 200 GLU cc_start: 0.8856 (pt0) cc_final: 0.8483 (pt0) REVERT: L 134 LEU cc_start: 0.9067 (tt) cc_final: 0.8419 (mp) REVERT: L 155 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: L 191 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7926 (m110) REVERT: M 174 TYR cc_start: 0.8742 (m-10) cc_final: 0.7976 (m-10) REVERT: M 201 LYS cc_start: 0.8717 (mtpm) cc_final: 0.8485 (mtpt) REVERT: M 212 LYS cc_start: 0.9019 (tttm) cc_final: 0.8736 (ttpp) REVERT: M 226 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7278 (ptp-170) REVERT: M 257 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8667 (pt0) REVERT: M 332 GLU cc_start: 0.8311 (pt0) cc_final: 0.8071 (pt0) REVERT: N 69 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8177 (mtt90) REVERT: N 106 MET cc_start: 0.8790 (mpt) cc_final: 0.8109 (mpt) REVERT: N 179 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8564 (mtt90) REVERT: N 183 LYS cc_start: 0.8923 (ttpt) cc_final: 0.8714 (tppp) REVERT: N 195 ARG cc_start: 0.8684 (mtp-110) cc_final: 0.8245 (mtp85) REVERT: N 203 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8027 (mt-10) REVERT: O 7 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7267 (p0) REVERT: O 93 GLU cc_start: 0.8150 (tt0) cc_final: 0.7640 (tm-30) REVERT: O 97 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: O 115 MET cc_start: 0.9217 (mmm) cc_final: 0.8949 (mmp) REVERT: O 125 GLN cc_start: 0.8309 (mt0) cc_final: 0.8081 (tt0) REVERT: O 173 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7820 (mmpt) REVERT: O 190 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8342 (mp) REVERT: O 236 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8172 (m110) REVERT: P 16 LYS cc_start: 0.8800 (ptmt) cc_final: 0.8051 (mmtm) REVERT: P 85 ILE cc_start: 0.9221 (mt) cc_final: 0.8938 (mt) REVERT: P 202 THR cc_start: 0.8906 (p) cc_final: 0.8553 (t) REVERT: Q 29 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: Q 53 HIS cc_start: 0.8736 (t-90) cc_final: 0.8270 (t-90) REVERT: Q 193 ASP cc_start: 0.8522 (t0) cc_final: 0.8236 (m-30) REVERT: Q 204 LYS cc_start: 0.8589 (tttt) cc_final: 0.8163 (tptp) REVERT: Q 266 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6630 (tm-30) REVERT: R 23 GLN cc_start: 0.8204 (mt0) cc_final: 0.7887 (mm-40) REVERT: R 49 SER cc_start: 0.6436 (t) cc_final: 0.5999 (p) REVERT: R 54 GLN cc_start: 0.8297 (pt0) cc_final: 0.7669 (mm110) REVERT: R 174 LYS cc_start: 0.7943 (mmtp) cc_final: 0.7649 (mtmm) REVERT: R 210 GLN cc_start: 0.9357 (OUTLIER) cc_final: 0.9078 (mt0) REVERT: R 213 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7737 (mp0) REVERT: R 215 ARG cc_start: 0.8475 (tmm-80) cc_final: 0.8225 (tmt90) REVERT: R 219 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: R 223 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.6931 (mm110) REVERT: S 118 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8377 (mp0) REVERT: S 249 LYS cc_start: 0.8756 (mmtm) cc_final: 0.8395 (mmmt) REVERT: S 313 GLU cc_start: 0.8755 (mp0) cc_final: 0.8470 (mp0) REVERT: S 336 LYS cc_start: 0.7999 (tttt) cc_final: 0.7554 (tppp) REVERT: T 190 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7745 (m-40) REVERT: T 279 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7804 (mm-30) REVERT: T 343 HIS cc_start: 0.7129 (m90) cc_final: 0.6744 (m-70) REVERT: T 347 CYS cc_start: 0.8668 (m) cc_final: 0.8283 (m) REVERT: T 395 ARG cc_start: 0.7042 (mtm-85) cc_final: 0.6619 (mtm-85) REVERT: T 404 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.5405 (ppt170) REVERT: U 94 GLN cc_start: 0.8559 (tt0) cc_final: 0.8237 (tm-30) REVERT: U 185 THR cc_start: 0.8937 (p) cc_final: 0.8663 (p) REVERT: U 188 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8330 (pt0) REVERT: V 140 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8409 (mtp) REVERT: V 143 MET cc_start: 0.8402 (ttp) cc_final: 0.8086 (mmp) REVERT: V 201 MET cc_start: 0.8810 (mtt) cc_final: 0.8554 (mtm) REVERT: V 273 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8064 (tppt) REVERT: W 61 ARG cc_start: 0.7746 (mtp85) cc_final: 0.7424 (mmt90) REVERT: W 82 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: W 119 TYR cc_start: 0.9000 (m-80) cc_final: 0.8794 (m-80) REVERT: W 225 MET cc_start: 0.7200 (mtp) cc_final: 0.6758 (mtt) REVERT: X 6 TYR cc_start: 0.9048 (t80) cc_final: 0.8785 (t80) REVERT: X 38 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8563 (mm-30) REVERT: X 134 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8242 (pm20) REVERT: X 183 TYR cc_start: 0.8933 (m-80) cc_final: 0.8339 (m-80) REVERT: Y 38 GLN cc_start: 0.9082 (tt0) cc_final: 0.8882 (tt0) REVERT: Y 40 ASP cc_start: 0.8627 (t0) cc_final: 0.8374 (t70) REVERT: Y 200 GLU cc_start: 0.8826 (pt0) cc_final: 0.8412 (pt0) REVERT: Z 131 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8130 (mmt) REVERT: Z 244 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8334 (mmtt) REVERT: Z 280 GLU cc_start: 0.8224 (pt0) cc_final: 0.7810 (mp0) REVERT: Z 281 LYS cc_start: 0.8699 (mttm) cc_final: 0.8367 (mtmt) REVERT: a 242 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8114 (mm-30) REVERT: b 100 ASP cc_start: 0.8135 (t70) cc_final: 0.7927 (OUTLIER) REVERT: b 106 MET cc_start: 0.8911 (mtt) cc_final: 0.8456 (mtt) REVERT: b 112 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6861 (ttt180) REVERT: b 115 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7483 (tm-30) outliers start: 236 outliers final: 144 residues processed: 1086 average time/residue: 1.6961 time to fit residues: 2272.1229 Evaluate side-chains 1121 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 934 time to evaluate : 5.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 402 LYS Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain J residue 12 MET Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 201 LYS Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain L residue 245 ASP Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 260 LEU Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 97 ASP Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain O residue 173 LYS Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 236 ASN Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 172 GLN Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 237 LYS Chi-restraints excluded: chain Q residue 268 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 223 GLN Chi-restraints excluded: chain S residue 107 GLU Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 132 LYS Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 184 ASP Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 243 VAL Chi-restraints excluded: chain T residue 348 THR Chi-restraints excluded: chain T residue 365 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 182 SER Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 188 GLU Chi-restraints excluded: chain U residue 227 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 140 MET Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 246 ASN Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 210 ASP Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain X residue 47 ASP Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain Y residue 12 ASP Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 152 GLN Chi-restraints excluded: chain Z residue 214 ASP Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain Z residue 249 GLU Chi-restraints excluded: chain a residue 154 ASN Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain a residue 219 SER Chi-restraints excluded: chain a residue 293 THR Chi-restraints excluded: chain a residue 327 ASP Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 112 ARG Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 192 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 540 optimal weight: 4.9990 chunk 568 optimal weight: 4.9990 chunk 518 optimal weight: 0.9980 chunk 553 optimal weight: 4.9990 chunk 333 optimal weight: 3.9990 chunk 241 optimal weight: 0.8980 chunk 434 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 499 optimal weight: 3.9990 chunk 523 optimal weight: 0.8980 chunk 551 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 100 ASN D 54 GLN D 187 HIS ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 GLN L 222 GLN ** L 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 70 GLN O 228 ASN P 200 GLN P 205 ASN R 223 GLN S 255 GLN T 195 ASN V 241 GLN V 246 ASN W 229 GLN ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 130 GLN a 180 ASN b 105 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 50122 Z= 0.331 Angle : 0.552 8.929 67810 Z= 0.290 Chirality : 0.044 0.179 7544 Planarity : 0.004 0.049 8790 Dihedral : 6.826 89.999 7100 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.03 % Favored : 97.90 % Rotamer: Outliers : 4.66 % Allowed : 22.68 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.10), residues: 6290 helix: 1.96 (0.11), residues: 2356 sheet: 0.01 (0.12), residues: 1580 loop : -0.02 (0.12), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 165 HIS 0.007 0.001 HIS D 187 PHE 0.017 0.002 PHE K 8 TYR 0.027 0.002 TYR J 96 ARG 0.009 0.000 ARG G 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 912 time to evaluate : 5.348 Fit side-chains revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8085 (mt0) cc_final: 0.7680 (mm-40) REVERT: A 161 TRP cc_start: 0.8685 (t60) cc_final: 0.8158 (t-100) REVERT: A 184 ARG cc_start: 0.8023 (tpp80) cc_final: 0.7469 (mmm160) REVERT: A 215 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8033 (mmmt) REVERT: A 217 LYS cc_start: 0.8582 (tttt) cc_final: 0.7974 (pttp) REVERT: B 3 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7059 (tt0) REVERT: B 21 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8416 (mt-10) REVERT: B 118 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8182 (tt0) REVERT: B 210 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8509 (ptt90) REVERT: C 35 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8736 (mm) REVERT: C 40 LYS cc_start: 0.8528 (mmtp) cc_final: 0.7936 (pttt) REVERT: C 196 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8817 (tt) REVERT: C 237 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8331 (tppt) REVERT: C 265 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7272 (tpt-90) REVERT: D 52 LYS cc_start: 0.8012 (mttp) cc_final: 0.7555 (mppt) REVERT: D 57 ARG cc_start: 0.7660 (tmm160) cc_final: 0.7252 (ptt90) REVERT: D 138 GLU cc_start: 0.8624 (tp30) cc_final: 0.8403 (mm-30) REVERT: D 177 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7905 (mmtp) REVERT: D 180 MET cc_start: 0.8276 (mtt) cc_final: 0.7894 (mtm) REVERT: D 215 ARG cc_start: 0.8436 (ttp-170) cc_final: 0.8002 (mtp-110) REVERT: D 221 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7129 (tp30) REVERT: D 232 GLU cc_start: 0.7222 (tt0) cc_final: 0.6765 (mt-10) REVERT: E 107 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6043 (mp0) REVERT: E 140 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8739 (mm) REVERT: E 190 GLU cc_start: 0.8431 (tp30) cc_final: 0.8196 (tp30) REVERT: E 278 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7542 (mt0) REVERT: E 300 ASP cc_start: 0.7932 (m-30) cc_final: 0.7307 (m-30) REVERT: E 342 MET cc_start: 0.6591 (ttm) cc_final: 0.6067 (ttm) REVERT: F 270 MET cc_start: 0.9089 (mmm) cc_final: 0.8693 (mmm) REVERT: F 402 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6815 (tptp) REVERT: G 13 ASP cc_start: 0.8661 (p0) cc_final: 0.8416 (p0) REVERT: G 44 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8173 (m-30) REVERT: G 51 GLU cc_start: 0.8155 (tt0) cc_final: 0.7883 (tm-30) REVERT: G 115 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8222 (mmt90) REVERT: H 123 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8623 (p0) REVERT: H 139 LYS cc_start: 0.8747 (ttmm) cc_final: 0.8411 (ttpp) REVERT: H 143 MET cc_start: 0.8254 (ttp) cc_final: 0.8013 (tpp) REVERT: H 201 MET cc_start: 0.8970 (mtt) cc_final: 0.8730 (mtt) REVERT: H 279 MET cc_start: 0.8956 (mtm) cc_final: 0.8547 (mtp) REVERT: I 118 ARG cc_start: 0.8843 (ttm170) cc_final: 0.8600 (ttp-110) REVERT: I 225 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6663 (mtt) REVERT: I 226 TYR cc_start: 0.7109 (t80) cc_final: 0.6483 (t80) REVERT: I 230 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7809 (mm-30) REVERT: J 4 MET cc_start: 0.9133 (mmm) cc_final: 0.8869 (mmt) REVERT: J 38 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8536 (mm-30) REVERT: J 97 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8251 (mt-10) REVERT: J 114 LYS cc_start: 0.8058 (tttt) cc_final: 0.7666 (mmtm) REVERT: K 1 MET cc_start: 0.7554 (mmm) cc_final: 0.7064 (mmm) REVERT: K 11 LYS cc_start: 0.9123 (tmmt) cc_final: 0.8909 (tttm) REVERT: K 22 ASN cc_start: 0.8902 (t0) cc_final: 0.8600 (t0) REVERT: K 196 LYS cc_start: 0.8696 (ptmm) cc_final: 0.8493 (ptmm) REVERT: K 200 GLU cc_start: 0.8877 (pt0) cc_final: 0.8572 (pt0) REVERT: L 134 LEU cc_start: 0.9143 (tt) cc_final: 0.8506 (mp) REVERT: L 155 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8356 (mp0) REVERT: L 191 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7931 (m110) REVERT: M 174 TYR cc_start: 0.8758 (m-10) cc_final: 0.8056 (m-10) REVERT: M 212 LYS cc_start: 0.9034 (tttm) cc_final: 0.8795 (ttpp) REVERT: M 257 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8699 (pt0) REVERT: M 281 ARG cc_start: 0.8518 (mtp85) cc_final: 0.7958 (mtp-110) REVERT: M 295 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8050 (mp0) REVERT: M 332 GLU cc_start: 0.8333 (pt0) cc_final: 0.8106 (pt0) REVERT: N 69 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8277 (mtt90) REVERT: N 106 MET cc_start: 0.8778 (mpt) cc_final: 0.8062 (mpt) REVERT: N 179 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8658 (mtt-85) REVERT: N 183 LYS cc_start: 0.8954 (ttpt) cc_final: 0.8731 (tppp) REVERT: N 195 ARG cc_start: 0.8713 (mtp-110) cc_final: 0.8332 (mtp85) REVERT: N 203 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: O 7 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7263 (p0) REVERT: O 93 GLU cc_start: 0.8148 (tt0) cc_final: 0.7647 (tm-30) REVERT: O 97 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: O 115 MET cc_start: 0.9247 (mmm) cc_final: 0.8996 (mmp) REVERT: O 125 GLN cc_start: 0.8385 (mt0) cc_final: 0.8139 (tt0) REVERT: O 173 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7830 (mmpt) REVERT: O 190 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8386 (mp) REVERT: O 236 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8183 (m110) REVERT: P 16 LYS cc_start: 0.8844 (ptmt) cc_final: 0.8067 (mmtm) REVERT: P 202 THR cc_start: 0.8886 (p) cc_final: 0.8514 (t) REVERT: Q 53 HIS cc_start: 0.8781 (t-90) cc_final: 0.8333 (t-90) REVERT: Q 193 ASP cc_start: 0.8531 (t0) cc_final: 0.8240 (m-30) REVERT: Q 204 LYS cc_start: 0.8583 (tttt) cc_final: 0.8233 (tptp) REVERT: Q 206 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8347 (mtp) REVERT: R 23 GLN cc_start: 0.8164 (mt0) cc_final: 0.7862 (mm-40) REVERT: R 49 SER cc_start: 0.6780 (t) cc_final: 0.6270 (p) REVERT: R 54 GLN cc_start: 0.8294 (pt0) cc_final: 0.7673 (mm110) REVERT: R 59 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7714 (mp) REVERT: R 174 LYS cc_start: 0.7971 (mmtp) cc_final: 0.7644 (mtmm) REVERT: R 210 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.9032 (mt0) REVERT: R 213 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7775 (mp0) REVERT: R 215 ARG cc_start: 0.8532 (tmm-80) cc_final: 0.8275 (tmt90) REVERT: R 219 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: S 118 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: S 249 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8415 (mmmt) REVERT: S 336 LYS cc_start: 0.8021 (tttt) cc_final: 0.7458 (tppp) REVERT: T 190 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7746 (m-40) REVERT: T 279 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7968 (mm-30) REVERT: T 343 HIS cc_start: 0.7205 (m90) cc_final: 0.6841 (m-70) REVERT: T 347 CYS cc_start: 0.8744 (m) cc_final: 0.8334 (m) REVERT: T 395 ARG cc_start: 0.7114 (mtm-85) cc_final: 0.6697 (mtm-85) REVERT: T 404 ARG cc_start: 0.5821 (OUTLIER) cc_final: 0.5398 (ppt170) REVERT: U 94 GLN cc_start: 0.8589 (tt0) cc_final: 0.8261 (tm-30) REVERT: V 140 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8424 (mtp) REVERT: V 143 MET cc_start: 0.8404 (ttp) cc_final: 0.8070 (mmp) REVERT: V 201 MET cc_start: 0.8830 (mtt) cc_final: 0.8544 (mtm) REVERT: V 273 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8097 (tppt) REVERT: W 61 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7436 (mmt90) REVERT: W 82 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8516 (tt0) REVERT: W 119 TYR cc_start: 0.9049 (m-80) cc_final: 0.8815 (m-80) REVERT: W 225 MET cc_start: 0.7265 (mtp) cc_final: 0.7054 (mtm) REVERT: X 6 TYR cc_start: 0.9051 (t80) cc_final: 0.8761 (t80) REVERT: X 31 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8013 (mm-40) REVERT: X 38 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8606 (mm-30) REVERT: X 134 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8334 (pm20) REVERT: Y 38 GLN cc_start: 0.9119 (tt0) cc_final: 0.8912 (tt0) REVERT: Y 40 ASP cc_start: 0.8644 (t0) cc_final: 0.8406 (t70) REVERT: Y 200 GLU cc_start: 0.8839 (pt0) cc_final: 0.8422 (pt0) REVERT: Z 131 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8128 (mmt) REVERT: Z 244 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8423 (mmtt) REVERT: Z 280 GLU cc_start: 0.8240 (pt0) cc_final: 0.7837 (mp0) REVERT: Z 281 LYS cc_start: 0.8650 (mttm) cc_final: 0.8272 (mtmt) REVERT: a 242 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8009 (mm-30) REVERT: b 100 ASP cc_start: 0.8195 (t70) cc_final: 0.7968 (t70) REVERT: b 106 MET cc_start: 0.8906 (mtt) cc_final: 0.8442 (mtt) REVERT: b 112 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6898 (ttt180) REVERT: b 115 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7231 (tm-30) outliers start: 244 outliers final: 154 residues processed: 1059 average time/residue: 1.7058 time to fit residues: 2227.2835 Evaluate side-chains 1085 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 889 time to evaluate : 5.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 402 LYS Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain J residue 12 MET Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 201 LYS Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain L residue 245 ASP Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 260 LEU Chi-restraints excluded: chain M residue 317 ASP Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 115 GLU Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 97 ASP Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain O residue 173 LYS Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 236 ASN Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 180 MET Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 172 GLN Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 206 MET Chi-restraints excluded: chain Q residue 268 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain S residue 107 GLU Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 132 LYS Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 184 ASP Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 243 VAL Chi-restraints excluded: chain T residue 348 THR Chi-restraints excluded: chain T residue 365 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 182 SER Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 188 GLU Chi-restraints excluded: chain U residue 227 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 140 MET Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 252 MET Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 210 ASP Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain X residue 31 GLN Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain Y residue 12 ASP Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 152 GLN Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain Z residue 249 GLU Chi-restraints excluded: chain a residue 154 ASN Chi-restraints excluded: chain a residue 219 SER Chi-restraints excluded: chain a residue 293 THR Chi-restraints excluded: chain a residue 327 ASP Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 112 ARG Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 192 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 363 optimal weight: 0.9990 chunk 585 optimal weight: 2.9990 chunk 357 optimal weight: 0.4980 chunk 277 optimal weight: 0.7980 chunk 406 optimal weight: 0.9990 chunk 613 optimal weight: 1.9990 chunk 564 optimal weight: 1.9990 chunk 488 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 377 optimal weight: 0.0370 chunk 299 optimal weight: 1.9990 overall best weight: 0.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 100 ASN D 54 GLN D 97 ASN D 187 HIS ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN G 147 GLN I 247 GLN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 222 GLN L 291 GLN N 70 GLN O 228 ASN P 200 GLN P 205 ASN R 223 GLN S 255 GLN T 195 ASN V 241 GLN W 229 GLN X 169 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 130 GLN a 180 ASN b 62 GLN b 105 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 50122 Z= 0.162 Angle : 0.498 9.550 67810 Z= 0.263 Chirality : 0.041 0.170 7544 Planarity : 0.004 0.047 8790 Dihedral : 6.564 89.995 7100 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.86 % Favored : 98.08 % Rotamer: Outliers : 3.44 % Allowed : 23.92 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.10), residues: 6290 helix: 2.16 (0.11), residues: 2338 sheet: 0.03 (0.12), residues: 1568 loop : -0.00 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 154 HIS 0.007 0.001 HIS D 187 PHE 0.017 0.001 PHE K 8 TYR 0.021 0.001 TYR J 96 ARG 0.009 0.000 ARG G 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 957 time to evaluate : 5.631 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8279 (t70) cc_final: 0.8056 (p0) REVERT: A 125 GLN cc_start: 0.7997 (mt0) cc_final: 0.7631 (mm-40) REVERT: A 161 TRP cc_start: 0.8624 (t60) cc_final: 0.8095 (t-100) REVERT: A 184 ARG cc_start: 0.7979 (tpp80) cc_final: 0.7441 (mmm160) REVERT: A 217 LYS cc_start: 0.8529 (tttt) cc_final: 0.7975 (pttt) REVERT: B 21 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8361 (mt-10) REVERT: B 118 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8175 (tt0) REVERT: B 165 SER cc_start: 0.8591 (p) cc_final: 0.8297 (p) REVERT: B 181 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7493 (mt-10) REVERT: C 4 ARG cc_start: 0.8558 (mtp85) cc_final: 0.8324 (mtp-110) REVERT: C 40 LYS cc_start: 0.8521 (mmtp) cc_final: 0.7918 (pttt) REVERT: C 66 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8279 (m) REVERT: C 196 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8793 (tt) REVERT: C 237 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8356 (tppt) REVERT: C 265 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7207 (tpt-90) REVERT: D 57 ARG cc_start: 0.7419 (tmm160) cc_final: 0.6966 (ptt90) REVERT: D 138 GLU cc_start: 0.8545 (tp30) cc_final: 0.8327 (mm-30) REVERT: D 177 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7904 (mmtp) REVERT: D 180 MET cc_start: 0.8189 (mtt) cc_final: 0.7816 (mtm) REVERT: D 215 ARG cc_start: 0.8425 (ttp-170) cc_final: 0.7978 (mtp-110) REVERT: D 221 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7200 (tp30) REVERT: D 224 LYS cc_start: 0.8311 (mtmt) cc_final: 0.7855 (ptmt) REVERT: D 232 GLU cc_start: 0.7201 (tt0) cc_final: 0.6791 (mt-10) REVERT: E 107 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6095 (mp0) REVERT: E 190 GLU cc_start: 0.8370 (tp30) cc_final: 0.8129 (tp30) REVERT: E 278 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7492 (mt0) REVERT: E 300 ASP cc_start: 0.7866 (m-30) cc_final: 0.7264 (m-30) REVERT: E 342 MET cc_start: 0.6576 (ttm) cc_final: 0.6025 (ttm) REVERT: F 270 MET cc_start: 0.8906 (mmm) cc_final: 0.8553 (mmm) REVERT: F 402 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6775 (tptp) REVERT: G 13 ASP cc_start: 0.8669 (p0) cc_final: 0.8442 (p0) REVERT: G 44 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: G 51 GLU cc_start: 0.8123 (tt0) cc_final: 0.7875 (tm-30) REVERT: G 115 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8239 (mmt90) REVERT: H 123 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8589 (p0) REVERT: H 139 LYS cc_start: 0.8678 (ttmm) cc_final: 0.8373 (ttpp) REVERT: H 201 MET cc_start: 0.8966 (mtt) cc_final: 0.8607 (mtm) REVERT: I 118 ARG cc_start: 0.8829 (ttm170) cc_final: 0.8570 (ttp-110) REVERT: I 225 MET cc_start: 0.7244 (mtp) cc_final: 0.6986 (mtt) REVERT: I 226 TYR cc_start: 0.7075 (t80) cc_final: 0.6503 (t80) REVERT: I 230 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7744 (mm-30) REVERT: J 4 MET cc_start: 0.9114 (mmm) cc_final: 0.8863 (mmt) REVERT: J 38 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8523 (mm-30) REVERT: J 75 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8535 (mmtt) REVERT: J 97 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8207 (mt-10) REVERT: J 114 LYS cc_start: 0.7968 (tttt) cc_final: 0.7661 (mmtm) REVERT: K 1 MET cc_start: 0.7535 (mmm) cc_final: 0.7056 (mmm) REVERT: K 22 ASN cc_start: 0.8891 (t0) cc_final: 0.8604 (t0) REVERT: K 181 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8417 (mpt180) REVERT: K 200 GLU cc_start: 0.8829 (pt0) cc_final: 0.8519 (pt0) REVERT: L 134 LEU cc_start: 0.9063 (tt) cc_final: 0.8415 (mp) REVERT: L 155 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: L 191 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7927 (m110) REVERT: M 174 TYR cc_start: 0.8722 (m-10) cc_final: 0.7957 (m-10) REVERT: M 201 LYS cc_start: 0.8754 (mtpm) cc_final: 0.8539 (mtpp) REVERT: M 212 LYS cc_start: 0.8997 (tttm) cc_final: 0.8720 (ttpp) REVERT: M 226 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7235 (ptp-170) REVERT: M 257 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8618 (pt0) REVERT: M 295 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8004 (mp0) REVERT: M 332 GLU cc_start: 0.8294 (pt0) cc_final: 0.7991 (pt0) REVERT: N 34 ASN cc_start: 0.9284 (p0) cc_final: 0.9066 (p0) REVERT: N 106 MET cc_start: 0.8760 (mpt) cc_final: 0.8102 (mpt) REVERT: N 183 LYS cc_start: 0.8918 (ttpt) cc_final: 0.8572 (tppt) REVERT: N 195 ARG cc_start: 0.8679 (mtp-110) cc_final: 0.8311 (mtp85) REVERT: N 203 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: O 7 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7216 (p0) REVERT: O 115 MET cc_start: 0.9183 (mmm) cc_final: 0.8911 (mmp) REVERT: O 125 GLN cc_start: 0.8288 (mt0) cc_final: 0.8012 (mm-40) REVERT: O 173 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7811 (mmpt) REVERT: O 190 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8303 (mp) REVERT: O 236 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8174 (m110) REVERT: P 16 LYS cc_start: 0.8757 (ptmt) cc_final: 0.7964 (mmtm) REVERT: P 85 ILE cc_start: 0.9220 (mt) cc_final: 0.8922 (mt) REVERT: P 167 ASP cc_start: 0.8527 (m-30) cc_final: 0.8162 (m-30) REVERT: P 202 THR cc_start: 0.8915 (p) cc_final: 0.8537 (t) REVERT: Q 53 HIS cc_start: 0.8755 (t-90) cc_final: 0.8315 (t-90) REVERT: Q 193 ASP cc_start: 0.8515 (t0) cc_final: 0.8244 (m-30) REVERT: Q 204 LYS cc_start: 0.8569 (tttt) cc_final: 0.8143 (tptp) REVERT: Q 206 MET cc_start: 0.8706 (ptm) cc_final: 0.8485 (mtp) REVERT: R 23 GLN cc_start: 0.8198 (mt0) cc_final: 0.7880 (mm-40) REVERT: R 49 SER cc_start: 0.6432 (t) cc_final: 0.6034 (p) REVERT: R 54 GLN cc_start: 0.8274 (pt0) cc_final: 0.7675 (mm110) REVERT: R 59 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7642 (mp) REVERT: R 174 LYS cc_start: 0.7938 (mmtp) cc_final: 0.7652 (mtmm) REVERT: R 213 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7816 (mp0) REVERT: R 215 ARG cc_start: 0.8493 (tmm-80) cc_final: 0.8250 (tmt90) REVERT: R 219 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: R 223 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6862 (mm110) REVERT: S 107 GLU cc_start: 0.5538 (OUTLIER) cc_final: 0.5308 (mm-30) REVERT: S 249 LYS cc_start: 0.8760 (mmtm) cc_final: 0.8401 (mmmt) REVERT: S 313 GLU cc_start: 0.8660 (mp0) cc_final: 0.8440 (mp0) REVERT: S 336 LYS cc_start: 0.7981 (tttt) cc_final: 0.7520 (tppp) REVERT: T 279 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7751 (mm-30) REVERT: T 343 HIS cc_start: 0.7101 (m90) cc_final: 0.6711 (m-70) REVERT: T 347 CYS cc_start: 0.8637 (m) cc_final: 0.8247 (m) REVERT: T 395 ARG cc_start: 0.7106 (mtm-85) cc_final: 0.6694 (mtm-85) REVERT: T 404 ARG cc_start: 0.5964 (OUTLIER) cc_final: 0.5439 (ppt170) REVERT: U 94 GLN cc_start: 0.8568 (tt0) cc_final: 0.8250 (tm-30) REVERT: U 188 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: V 140 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8434 (mtp) REVERT: V 143 MET cc_start: 0.8383 (ttp) cc_final: 0.8078 (mmp) REVERT: V 201 MET cc_start: 0.8786 (mtt) cc_final: 0.8547 (mtm) REVERT: V 273 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8059 (tppt) REVERT: W 61 ARG cc_start: 0.7645 (mtp85) cc_final: 0.7413 (mmt180) REVERT: W 82 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: W 225 MET cc_start: 0.7185 (mtp) cc_final: 0.6717 (mtt) REVERT: X 6 TYR cc_start: 0.9022 (t80) cc_final: 0.8768 (t80) REVERT: X 17 LYS cc_start: 0.8816 (tttm) cc_final: 0.8547 (ttmm) REVERT: X 38 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8563 (mm-30) REVERT: X 134 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8246 (pm20) REVERT: X 183 TYR cc_start: 0.8885 (m-80) cc_final: 0.8314 (m-80) REVERT: Y 40 ASP cc_start: 0.8616 (t0) cc_final: 0.8362 (t70) REVERT: Y 200 GLU cc_start: 0.8807 (pt0) cc_final: 0.8397 (pt0) REVERT: Z 131 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8111 (mmt) REVERT: Z 196 MET cc_start: 0.9139 (ptp) cc_final: 0.8688 (ptm) REVERT: Z 244 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8270 (mmtt) REVERT: Z 280 GLU cc_start: 0.8256 (pt0) cc_final: 0.7828 (mp0) REVERT: Z 281 LYS cc_start: 0.8689 (mttm) cc_final: 0.8326 (mtmt) REVERT: a 292 MET cc_start: 0.8351 (tpp) cc_final: 0.8016 (tpt) REVERT: b 100 ASP cc_start: 0.8117 (t70) cc_final: 0.7904 (t70) REVERT: b 106 MET cc_start: 0.8915 (mtt) cc_final: 0.8441 (mtt) REVERT: b 112 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6827 (ttt180) REVERT: b 115 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7303 (tm-30) outliers start: 180 outliers final: 110 residues processed: 1062 average time/residue: 1.7236 time to fit residues: 2257.3852 Evaluate side-chains 1071 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 926 time to evaluate : 5.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 396 LYS Chi-restraints excluded: chain F residue 402 LYS Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain J residue 12 MET Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 260 LEU Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 42 LYS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 173 LYS Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 236 ASN Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 223 GLN Chi-restraints excluded: chain S residue 107 GLU Chi-restraints excluded: chain S residue 132 LYS Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 184 ASP Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain T residue 365 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 188 GLU Chi-restraints excluded: chain U residue 227 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 140 MET Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 273 LYS Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain W residue 210 ASP Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain X residue 47 ASP Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 121 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain Z residue 131 MET Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 244 LYS Chi-restraints excluded: chain a residue 154 ASN Chi-restraints excluded: chain a residue 219 SER Chi-restraints excluded: chain a residue 293 THR Chi-restraints excluded: chain a residue 327 ASP Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 112 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 388 optimal weight: 3.9990 chunk 520 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 450 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 489 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 502 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 100 ASN D 187 HIS ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN K 102 GLN ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 GLN ** L 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 70 GLN O 228 ASN P 205 ASN R 223 GLN T 195 ASN ** T 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 GLN W 229 GLN ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 130 GLN a 180 ASN b 105 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.107959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.090512 restraints weight = 62921.700| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.30 r_work: 0.2816 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 50122 Z= 0.327 Angle : 0.553 11.097 67810 Z= 0.290 Chirality : 0.044 0.221 7544 Planarity : 0.004 0.051 8790 Dihedral : 6.601 89.848 7083 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.97 % Favored : 97.97 % Rotamer: Outliers : 3.44 % Allowed : 24.15 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.10), residues: 6290 helix: 1.98 (0.11), residues: 2356 sheet: 0.04 (0.12), residues: 1576 loop : -0.02 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 165 HIS 0.008 0.001 HIS D 187 PHE 0.018 0.002 PHE K 8 TYR 0.027 0.002 TYR J 96 ARG 0.010 0.001 ARG N 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30731.33 seconds wall clock time: 537 minutes 41.45 seconds (32261.45 seconds total)