Starting phenix.real_space_refine on Sun Feb 25 05:15:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/02_2024/8olu_16963_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/02_2024/8olu_16963.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/02_2024/8olu_16963_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/02_2024/8olu_16963_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/02_2024/8olu_16963_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/02_2024/8olu_16963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/02_2024/8olu_16963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/02_2024/8olu_16963_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/02_2024/8olu_16963_updated.pdb" } resolution = 2.59 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= 0.014 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: 4 Type Number sf(0) Gaussians S 328 5.16 5 C 30760 2.51 5 N 8424 2.21 5 O 9418 1.98 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 ARG 59": "NH1" <-> "NH2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ASP 146": "OD1" <-> "OD2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ARG 97": "NH1" <-> "NH2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ASP 214": "OD1" <-> "OD2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D ARG 57": "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 ARG 81": "NH1" <-> "NH2" 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 ARG 157": "NH1" <-> "NH2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 215": "NH1" <-> "NH2" Residue "D TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E GLU 151": "OE1" <-> "OE2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E ARG 186": "NH1" <-> "NH2" Residue "E GLU 195": "OE1" <-> "OE2" Residue "E GLU 248": "OE1" <-> "OE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 295": "OE1" <-> "OE2" Residue "E GLU 313": "OE1" <-> "OE2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E ASP 323": "OD1" <-> "OD2" Residue "E ASP 324": "OD1" <-> "OD2" Residue "E GLU 334": "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 247": "NH1" <-> "NH2" 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 ARG 304": "NH1" <-> "NH2" Residue "F ASP 317": "OD1" <-> "OD2" Residue "F ASP 320": "OD1" <-> "OD2" Residue "F ARG 334": "NH1" <-> "NH2" 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 GLU 351": "OE1" <-> "OE2" Residue "F ASP 383": "OD1" <-> "OD2" Residue "F PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 399": "OD1" <-> "OD2" Residue "G ASP 9": "OD1" <-> "OD2" Residue "G ASP 13": "OD1" <-> "OD2" Residue "G GLU 18": "OE1" <-> "OE2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G ARG 86": "NH1" <-> "NH2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G ARG 108": "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 TYR 129": "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 GLU 177": "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 "H TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 99": "NH1" <-> "NH2" Residue "H ARG 112": "NH1" <-> "NH2" Residue "H ARG 247": "NH1" <-> "NH2" Residue "H ARG 278": "NH1" <-> "NH2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "I TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "I GLU 178": "OE1" <-> "OE2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I ARG 189": "NH1" <-> "NH2" Residue "I ARG 224": "NH1" <-> "NH2" Residue "I ARG 228": "NH1" <-> "NH2" Residue "I ARG 246": "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 GLU 72": "OE1" <-> "OE2" Residue "J GLU 78": "OE1" <-> "OE2" Residue "J GLU 79": "OE1" <-> "OE2" Residue "J ARG 99": "NH1" <-> "NH2" Residue "J GLU 144": "OE1" <-> "OE2" Residue "J GLU 151": "OE1" <-> "OE2" Residue "J ARG 155": "NH1" <-> "NH2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "J GLU 165": "OE1" <-> "OE2" Residue "K GLU 3": "OE1" <-> "OE2" Residue "K ARG 9": "NH1" <-> "NH2" Residue "K TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 50": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K ARG 71": "NH1" <-> "NH2" Residue "K ARG 87": "NH1" <-> "NH2" Residue "K TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 106": "NH1" <-> "NH2" 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 GLU 249": "OE1" <-> "OE2" Residue "L ARG 256": "NH1" <-> "NH2" Residue "L TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "M ARG 186": "NH1" <-> "NH2" Residue "M ARG 196": "NH1" <-> "NH2" Residue "M ARG 226": "NH1" <-> "NH2" Residue "M GLU 242": "OE1" <-> "OE2" Residue "M GLU 257": "OE1" <-> "OE2" Residue "M ARG 264": "NH1" <-> "NH2" Residue "M GLU 291": "OE1" <-> "OE2" Residue "M GLU 296": "OE1" <-> "OE2" Residue "M GLU 310": "OE1" <-> "OE2" Residue "M GLU 332": "OE1" <-> "OE2" Residue "M ARG 337": "NH1" <-> "NH2" Residue "N TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 77": "OD1" <-> "OD2" Residue "N ARG 90": "NH1" <-> "NH2" Residue "N GLU 129": "OE1" <-> "OE2" Residue "N ARG 159": "NH1" <-> "NH2" Residue "N GLU 161": "OE1" <-> "OE2" Residue "N ARG 164": "NH1" <-> "NH2" Residue "N ARG 171": "NH1" <-> "NH2" Residue "N ARG 179": "NH1" <-> "NH2" Residue "N ARG 220": "NH1" <-> "NH2" Residue "O PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 40": "NH1" <-> "NH2" Residue "O ARG 56": "NH1" <-> "NH2" Residue "O ARG 59": "NH1" <-> "NH2" Residue "O TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 90": "NH1" <-> "NH2" Residue "O GLU 93": "OE1" <-> "OE2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 105": "OE1" <-> "OE2" Residue "O ARG 122": "NH1" <-> "NH2" Residue "O ASP 146": "OD1" <-> "OD2" Residue "O ASP 157": "OD1" <-> "OD2" Residue "O GLU 176": "OE1" <-> "OE2" Residue "O PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 182": "OE1" <-> "OE2" Residue "O ARG 184": "NH1" <-> "NH2" Residue "O GLU 218": "OE1" <-> "OE2" Residue "P GLU 21": "OE1" <-> "OE2" Residue "P PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 101": "OE1" <-> "OE2" Residue "P ARG 110": "NH1" <-> "NH2" Residue "P PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 126": "NH1" <-> "NH2" Residue "P ASP 167": "OD1" <-> "OD2" Residue "P PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 173": "OE1" <-> "OE2" Residue "P ARG 175": "NH1" <-> "NH2" Residue "P PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 215": "NH1" <-> "NH2" Residue "P GLU 217": "OE1" <-> "OE2" Residue "P ASP 222": "OD1" <-> "OD2" Residue "P ARG 225": "NH1" <-> "NH2" Residue "P ASP 226": "OD1" <-> "OD2" Residue "Q ARG 4": "NH1" <-> "NH2" Residue "Q ARG 17": "NH1" <-> "NH2" Residue "Q GLU 59": "OE1" <-> "OE2" Residue "Q ASP 63": "OD1" <-> "OD2" Residue "Q GLU 69": "OE1" <-> "OE2" Residue "Q ARG 97": "NH1" <-> "NH2" Residue "Q TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 184": "OD1" <-> "OD2" Residue "Q GLU 187": "OE1" <-> "OE2" Residue "Q ARG 200": "NH1" <-> "NH2" Residue "Q ASP 214": "OD1" <-> "OD2" Residue "Q ARG 215": "NH1" <-> "NH2" Residue "Q ARG 222": "NH1" <-> "NH2" Residue "Q ARG 265": "NH1" <-> "NH2" Residue "R GLU 24": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R ASP 55": "OD1" <-> "OD2" Residue "R ARG 57": "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 ARG 81": "NH1" <-> "NH2" 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 ARG 157": "NH1" <-> "NH2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 182": "NH1" <-> "NH2" Residue "R PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 215": "NH1" <-> "NH2" Residue "R TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 228": "OE1" <-> "OE2" Residue "R GLU 230": "OE1" <-> "OE2" Residue "R GLU 232": "OE1" <-> "OE2" Residue "R ARG 233": "NH1" <-> "NH2" Residue "R GLU 234": "OE1" <-> "OE2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "S PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 118": "OE1" <-> "OE2" Residue "S GLU 151": "OE1" <-> "OE2" Residue "S ARG 153": "NH1" <-> "NH2" Residue "S ARG 186": "NH1" <-> "NH2" Residue "S GLU 195": "OE1" <-> "OE2" Residue "S GLU 248": "OE1" <-> "OE2" Residue "S GLU 283": "OE1" <-> "OE2" Residue "S TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 295": "OE1" <-> "OE2" Residue "S GLU 313": "OE1" <-> "OE2" Residue "S ARG 321": "NH1" <-> "NH2" Residue "S ASP 323": "OD1" <-> "OD2" Residue "S ASP 324": "OD1" <-> "OD2" Residue "S GLU 334": "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 247": "NH1" <-> "NH2" 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 ARG 304": "NH1" <-> "NH2" Residue "T ASP 317": "OD1" <-> "OD2" Residue "T ASP 320": "OD1" <-> "OD2" Residue "T ARG 334": "NH1" <-> "NH2" 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 GLU 351": "OE1" <-> "OE2" Residue "T ASP 383": "OD1" <-> "OD2" Residue "T PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 399": "OD1" <-> "OD2" Residue "U ASP 9": "OD1" <-> "OD2" Residue "U ASP 13": "OD1" <-> "OD2" Residue "U GLU 18": "OE1" <-> "OE2" Residue "U ARG 20": "NH1" <-> "NH2" Residue "U GLU 51": "OE1" <-> "OE2" Residue "U GLU 60": "OE1" <-> "OE2" Residue "U ARG 72": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 91": "NH1" <-> "NH2" Residue "U GLU 97": "OE1" <-> "OE2" Residue "U ARG 108": "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 TYR 129": "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 GLU 177": "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 "V TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 99": "NH1" <-> "NH2" Residue "V ARG 112": "NH1" <-> "NH2" Residue "V ARG 247": "NH1" <-> "NH2" Residue "V ARG 278": "NH1" <-> "NH2" Residue "W ARG 59": "NH1" <-> "NH2" Residue "W ARG 61": "NH1" <-> "NH2" Residue "W TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 104": "NH1" <-> "NH2" Residue "W GLU 178": "OE1" <-> "OE2" Residue "W GLU 182": "OE1" <-> "OE2" Residue "W ARG 189": "NH1" <-> "NH2" Residue "W ARG 224": "NH1" <-> "NH2" Residue "W ARG 228": "NH1" <-> "NH2" Residue "W ARG 246": "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 GLU 72": "OE1" <-> "OE2" Residue "X GLU 78": "OE1" <-> "OE2" Residue "X GLU 79": "OE1" <-> "OE2" Residue "X ARG 99": "NH1" <-> "NH2" Residue "X GLU 144": "OE1" <-> "OE2" Residue "X GLU 151": "OE1" <-> "OE2" Residue "X ARG 155": "NH1" <-> "NH2" Residue "X GLU 161": "OE1" <-> "OE2" Residue "X GLU 165": "OE1" <-> "OE2" Residue "Y GLU 3": "OE1" <-> "OE2" Residue "Y ARG 9": "NH1" <-> "NH2" Residue "Y TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 50": "OE1" <-> "OE2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Y ARG 69": "NH1" <-> "NH2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ARG 87": "NH1" <-> "NH2" Residue "Y TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 106": "NH1" <-> "NH2" 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 GLU 249": "OE1" <-> "OE2" Residue "Z ARG 256": "NH1" <-> "NH2" Residue "Z TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a ARG 186": "NH1" <-> "NH2" Residue "a ARG 196": "NH1" <-> "NH2" Residue "a ARG 226": "NH1" <-> "NH2" Residue "a GLU 242": "OE1" <-> "OE2" Residue "a GLU 257": "OE1" <-> "OE2" Residue "a ARG 264": "NH1" <-> "NH2" Residue "a GLU 291": "OE1" <-> "OE2" Residue "a GLU 296": "OE1" <-> "OE2" Residue "a GLU 310": "OE1" <-> "OE2" Residue "a GLU 332": "OE1" <-> "OE2" Residue "a ARG 337": "NH1" <-> "NH2" Residue "b TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 77": "OD1" <-> "OD2" Residue "b ARG 90": "NH1" <-> "NH2" Residue "b GLU 129": "OE1" <-> "OE2" Residue "b ARG 159": "NH1" <-> "NH2" Residue "b GLU 161": "OE1" <-> "OE2" Residue "b ARG 164": "NH1" <-> "NH2" Residue "b ARG 171": "NH1" <-> "NH2" Residue "b ARG 179": "NH1" <-> "NH2" Residue "b ARG 220": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 48930 Number of models: 1 Model: "" Number of chains: 30 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: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2150 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain: "D" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1840 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 4, 'TRANS': 229} 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: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1819 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain: "G" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1714 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "H" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1705 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 8, 'TRANS': 219} 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: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1732 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 212} 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: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2150 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain: "R" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1840 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 4, 'TRANS': 229} 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: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1819 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain: "U" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1714 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "V" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1705 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 8, 'TRANS': 219} 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: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1732 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 212} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'VYW': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'VYW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.28, per 1000 atoms: 0.50 Number of scatterers: 48930 At special positions: 0 Unit cell: (187.25, 189.39, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 328 16.00 O 9418 8.00 N 8424 7.00 C 30760 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: 18.45 Conformation dependent library (CDL) restraints added in 9.1 seconds 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11648 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 166 helices and 68 sheets defined 34.5% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.56 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 removed outlier: 3.657A pdb=" N VAL A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.874A 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 123 removed outlier: 3.617A pdb=" N ARG A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.819A pdb=" N SER A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 195 through 210 Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 236 through 248 Processing helix chain 'B' and resid 18 through 28 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 Processing helix chain 'B' and resid 105 through 120 Processing helix chain 'B' and resid 165 through 175 removed outlier: 3.548A pdb=" N LYS B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.112A pdb=" N GLY B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 228 removed outlier: 3.544A 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: 3.972A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 184 removed outlier: 3.555A pdb=" N LYS C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.605A 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 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 251 through 266 Proline residue: C 256 - end of helix removed outlier: 3.778A pdb=" N ALA C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 26 Processing helix chain 'D' and resid 77 through 98 Processing helix chain 'D' and resid 104 through 119 Processing helix chain 'D' and resid 165 through 175 Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.566A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 230 removed outlier: 3.570A pdb=" N GLN D 223 " --> pdb=" O GLU D 219 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 131 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 182 through 203 removed outlier: 3.517A pdb=" N ILE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 219 removed outlier: 4.312A pdb=" N LEU E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 removed outlier: 3.526A pdb=" N ALA E 277 " --> pdb=" O ALA E 274 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER E 279 " --> pdb=" O ALA E 276 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE E 281 " --> pdb=" O GLN E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 305 Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'F' and resid 184 through 194 removed outlier: 3.500A pdb=" N GLU F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) removed outlier: 3.626A 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 284 removed outlier: 3.752A pdb=" N HIS F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 343 removed outlier: 3.545A pdb=" N HIS F 340 " --> pdb=" O TYR F 336 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLU F 342 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N HIS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 361 Processing helix chain 'F' and resid 391 through 397 removed outlier: 3.709A pdb=" N ARG F 395 " --> pdb=" O GLU F 391 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS F 396 " --> pdb=" O GLU F 392 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR F 397 " --> pdb=" O SER F 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 391 through 397' Processing helix chain 'G' and resid 22 through 32 Processing helix chain 'G' and resid 82 through 102 Processing helix chain 'G' and resid 109 through 124 removed outlier: 3.753A pdb=" N TYR G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 4.010A 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: 3.731A pdb=" N GLY G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) 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 188 removed outlier: 3.846A pdb=" N ILE H 187 " --> pdb=" O SER H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 196 Processing helix chain 'H' and resid 203 through 220 removed outlier: 3.607A 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 Processing helix chain 'I' and resid 105 through 118 Processing helix chain 'I' and resid 160 through 170 removed outlier: 3.537A pdb=" N GLN I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 192 removed outlier: 3.539A pdb=" N GLY I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 78 Processing helix chain 'J' and resid 84 through 96 Processing helix chain 'J' and resid 143 through 153 Processing helix chain 'J' and resid 160 through 177 removed outlier: 3.803A pdb=" N ARG J 177 " --> pdb=" O SER J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 70 Processing helix chain 'K' and resid 79 through 95 removed outlier: 3.985A pdb=" N ARG K 95 " --> pdb=" O ALA K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 157 removed outlier: 4.159A pdb=" N CYS K 148 " --> pdb=" O TYR K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 181 Processing helix chain 'L' and resid 148 through 169 Processing helix chain 'L' and resid 175 through 188 Processing helix chain 'L' and resid 231 through 241 removed outlier: 3.880A pdb=" N GLY L 236 " --> pdb=" O ILE L 232 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL L 237 " --> pdb=" O TYR L 233 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR L 240 " --> pdb=" O GLY L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 265 Processing helix chain 'L' and resid 291 through 298 Processing helix chain 'M' and resid 183 through 204 Processing helix chain 'M' and resid 211 through 225 removed outlier: 3.513A pdb=" N ARG M 225 " --> pdb=" O MET M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 268 through 279 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 141 removed outlier: 3.539A pdb=" N ILE N 141 " --> pdb=" O GLY N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 152 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 30 removed outlier: 3.657A pdb=" N VAL O 29 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 3.866A 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 123 removed outlier: 3.613A pdb=" N ARG O 122 " --> pdb=" O LYS O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 187 removed outlier: 3.815A pdb=" N SER O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 190 through 192 No H-bonds generated for 'chain 'O' and resid 190 through 192' Processing helix chain 'O' and resid 195 through 210 Processing helix chain 'O' and resid 216 through 218 No H-bonds generated for 'chain 'O' and resid 216 through 218' 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 Processing helix chain 'P' and resid 105 through 120 Processing helix chain 'P' and resid 165 through 175 removed outlier: 3.551A pdb=" N LYS P 174 " --> pdb=" O ALA P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 196 removed outlier: 4.112A pdb=" N GLY P 196 " --> pdb=" O THR P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 228 removed outlier: 3.544A 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: 3.974A pdb=" N TYR Q 127 " --> pdb=" O GLU Q 123 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR Q 128 " --> pdb=" O LYS Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 184 removed outlier: 3.557A pdb=" N LYS Q 183 " --> pdb=" O ALA Q 179 " (cutoff:3.500A) removed outlier: 3.613A 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 213 through 215 No H-bonds generated for 'chain 'Q' and resid 213 through 215' Processing helix chain 'Q' and resid 251 through 266 Proline residue: Q 256 - end of helix removed outlier: 3.772A pdb=" N ALA Q 264 " --> pdb=" O ARG Q 260 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 26 Processing helix chain 'R' and resid 77 through 98 Processing helix chain 'R' and resid 104 through 119 Processing helix chain 'R' and resid 165 through 175 Processing helix chain 'R' and resid 182 through 195 removed outlier: 3.568A pdb=" N GLU R 195 " --> pdb=" O LYS R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 230 removed outlier: 3.578A pdb=" N GLN R 223 " --> pdb=" O GLU R 219 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE R 225 " --> pdb=" O GLU R 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 131 Processing helix chain 'S' and resid 161 through 163 No H-bonds generated for 'chain 'S' and resid 161 through 163' Processing helix chain 'S' and resid 182 through 203 removed outlier: 3.518A pdb=" N ILE S 187 " --> pdb=" O ALA S 183 " (cutoff:3.500A) Processing helix chain 'S' and resid 209 through 219 removed outlier: 4.308A pdb=" N LEU S 219 " --> pdb=" O ALA S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 273 through 284 removed outlier: 3.530A pdb=" N ALA S 277 " --> pdb=" O ALA S 274 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER S 279 " --> pdb=" O ALA S 276 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE S 281 " --> pdb=" O GLN S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 291 through 305 Processing helix chain 'S' and resid 332 through 339 Processing helix chain 'T' and resid 184 through 194 removed outlier: 3.503A pdb=" N GLU T 191 " --> pdb=" O GLU T 187 " (cutoff:3.500A) removed outlier: 3.627A 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 284 removed outlier: 3.762A pdb=" N HIS T 284 " --> pdb=" O LYS T 280 " (cutoff:3.500A) Processing helix chain 'T' and resid 330 through 343 removed outlier: 3.538A pdb=" N HIS T 340 " --> pdb=" O TYR T 336 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU T 342 " --> pdb=" O GLU T 338 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N HIS T 343 " --> pdb=" O ARG T 339 " (cutoff:3.500A) Processing helix chain 'T' and resid 349 through 361 Processing helix chain 'T' and resid 391 through 397 removed outlier: 3.710A pdb=" N ARG T 395 " --> pdb=" O GLU T 391 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS T 396 " --> pdb=" O GLU T 392 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR T 397 " --> pdb=" O SER T 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 391 through 397' Processing helix chain 'U' and resid 22 through 32 Processing helix chain 'U' and resid 82 through 102 Processing helix chain 'U' and resid 109 through 124 removed outlier: 3.754A pdb=" N TYR U 123 " --> pdb=" O PHE U 119 " (cutoff:3.500A) removed outlier: 4.011A 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: 3.738A pdb=" N GLY U 191 " --> pdb=" O ASP U 187 " (cutoff:3.500A) 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 188 removed outlier: 3.849A pdb=" N ILE V 187 " --> pdb=" O SER V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 190 through 196 Processing helix chain 'V' and resid 203 through 220 removed outlier: 3.612A 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 removed outlier: 3.537A pdb=" N GLN W 166 " --> pdb=" O ALA W 162 " (cutoff:3.500A) Processing helix chain 'W' and resid 177 through 194 removed outlier: 3.538A pdb=" N GLY W 191 " --> pdb=" O ALA W 187 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 78 Processing helix chain 'X' and resid 84 through 96 Processing helix chain 'X' and resid 143 through 153 Processing helix chain 'X' and resid 160 through 177 removed outlier: 3.799A pdb=" N ARG X 177 " --> pdb=" O SER X 173 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 70 Processing helix chain 'Y' and resid 79 through 95 removed outlier: 3.992A pdb=" N ARG Y 95 " --> pdb=" O ALA Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 145 through 157 removed outlier: 4.163A pdb=" N CYS Y 148 " --> pdb=" O TYR Y 145 " (cutoff:3.500A) 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: 3.878A pdb=" N GLY Z 236 " --> pdb=" O ILE Z 232 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL Z 237 " --> pdb=" O TYR Z 233 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR Z 240 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) Processing helix chain 'Z' and resid 248 through 265 Processing helix chain 'Z' and resid 291 through 298 Processing helix chain 'a' and resid 183 through 204 Processing helix chain 'a' and resid 211 through 225 removed outlier: 3.514A pdb=" N ARG a 225 " --> pdb=" O MET a 221 " (cutoff:3.500A) Processing helix chain 'a' and resid 268 through 279 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 141 removed outlier: 3.538A pdb=" N ILE b 141 " --> pdb=" O GLY b 138 " (cutoff:3.500A) Processing helix chain 'b' and resid 143 through 152 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: 6.032A 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: 4.045A pdb=" N ILE A 153 " --> pdb=" O HIS A 165 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N CYS A 75 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLU A 68 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N MET A 77 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.030A 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 removed outlier: 3.506A pdb=" N GLY B 41 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 153 through 155 removed outlier: 6.134A pdb=" N CYS B 72 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL B 65 " --> pdb=" O CYS B 72 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR B 74 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 7.178A 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 164 removed outlier: 3.783A pdb=" N PHE C 140 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N CYS C 80 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LYS C 73 " --> pdb=" O CYS C 80 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL C 82 " --> pdb=" O MET C 71 " (cutoff:3.500A) removed outlier: 6.657A 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: 6.252A pdb=" N LEU D 71 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LYS D 64 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N PHE D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 7.804A 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: 4.742A pdb=" N VAL E 317 " --> pdb=" O TYR E 330 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 263 through 265 removed outlier: 4.012A pdb=" N LEU E 253 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP E 247 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA E 176 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU E 169 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N MET E 178 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 6.727A 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: 4.200A pdb=" N LEU F 309 " --> pdb=" O TYR F 321 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N MET F 237 " --> pdb=" O GLU F 230 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLU F 230 " --> pdb=" O MET F 237 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE F 239 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 5.937A 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 157 through 159 removed outlier: 3.686A pdb=" N ALA G 142 " --> pdb=" O GLY G 145 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE G 76 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ALA G 69 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE G 78 " --> pdb=" O ILE G 67 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE G 67 " --> pdb=" O ILE G 78 " (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: 4.088A pdb=" N VAL H 165 " --> pdb=" O LEU H 177 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE H 95 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N CYS H 97 " --> pdb=" O LYS H 90 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LYS H 90 " --> pdb=" O CYS H 97 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ARG H 99 " --> pdb=" O LEU H 88 " (cutoff:3.500A) removed outlier: 6.326A 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: 6.488A pdb=" N SER H 76 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 5.761A 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 156 Processing sheet with id= S, first strand: chain 'I' and resid 148 through 150 removed outlier: 5.560A pdb=" N CYS I 72 " --> pdb=" O TYR I 65 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR I 65 " --> pdb=" O CYS I 72 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLY I 74 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 6.530A 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: 6.411A pdb=" N GLU I 51 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 5.252A 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: 5.809A pdb=" N SER J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) removed outlier: 3.962A 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: 3.539A pdb=" N ASN J 46 " --> pdb=" O ILE J 49 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR J 51 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N VAL J 44 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU J 53 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 6.317A 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: 6.300A pdb=" N GLU J 30 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 5.579A 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: 4.207A 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: 6.291A pdb=" N VAL K 45 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLN K 38 " --> pdb=" O VAL K 45 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N CYS K 47 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILE K 36 " --> pdb=" O CYS K 47 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 21 through 24 removed outlier: 3.510A pdb=" N THR K 30 " --> pdb=" O ASN K 22 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE K 24 " --> pdb=" O LYS K 28 " (cutoff:3.500A) removed outlier: 5.157A 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: 6.419A pdb=" N HIS L 277 " --> pdb=" O LYS L 285 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LYS L 285 " --> pdb=" O HIS L 277 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N HIS L 279 " --> pdb=" O TRP L 283 " (cutoff:3.500A) removed outlier: 4.870A 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: 3.845A 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: 6.192A pdb=" N THR L 121 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE L 125 " --> pdb=" O THR L 121 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 263 through 265 removed outlier: 5.200A 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: 3.569A pdb=" N GLU M 257 " --> pdb=" O SER M 249 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER M 249 " --> pdb=" O GLU M 257 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN M 234 " --> pdb=" O TYR M 250 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N MET M 177 " --> pdb=" O GLN M 170 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLN M 170 " --> pdb=" O MET M 177 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N SER M 179 " --> pdb=" O ILE M 168 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE M 168 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 2 through 4 removed outlier: 6.478A pdb=" N TYR N 26 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ALA N 30 " --> pdb=" O TYR N 26 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 132 through 135 Processing sheet with id= AH, first strand: chain 'N' and resid 39 through 41 removed outlier: 3.501A pdb=" N SER N 45 " --> pdb=" O LEU N 41 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'O' and resid 167 through 171 removed outlier: 6.052A 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: 4.043A pdb=" N ILE O 153 " --> pdb=" O HIS O 165 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N CYS O 75 " --> pdb=" O GLU O 68 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLU O 68 " --> pdb=" O CYS O 75 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N MET O 77 " --> pdb=" O LEU O 66 " (cutoff:3.500A) removed outlier: 6.036A 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 Processing sheet with id= AL, first strand: chain 'P' and resid 153 through 155 removed outlier: 6.133A pdb=" N CYS P 72 " --> pdb=" O VAL P 65 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL P 65 " --> pdb=" O CYS P 72 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N TYR P 74 " --> pdb=" O VAL P 63 " (cutoff:3.500A) removed outlier: 7.181A 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 Processing sheet with id= AN, first strand: chain 'Q' and resid 162 through 164 removed outlier: 3.787A pdb=" N PHE Q 140 " --> pdb=" O THR Q 156 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N CYS Q 80 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS Q 73 " --> pdb=" O CYS Q 80 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL Q 82 " --> pdb=" O MET Q 71 " (cutoff:3.500A) removed outlier: 6.654A 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 153 through 155 removed outlier: 6.249A pdb=" N LEU R 71 " --> pdb=" O LYS R 64 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS R 64 " --> pdb=" O LEU R 71 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N PHE R 73 " --> pdb=" O ILE R 62 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE R 62 " --> pdb=" O PHE R 73 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'S' and resid 267 through 270 removed outlier: 4.735A pdb=" N VAL S 317 " --> pdb=" O TYR S 330 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'S' and resid 263 through 265 removed outlier: 4.015A pdb=" N LEU S 253 " --> pdb=" O TYR S 265 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP S 247 " --> pdb=" O GLY S 250 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA S 176 " --> pdb=" O GLU S 169 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU S 169 " --> pdb=" O ALA S 176 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N MET S 178 " --> pdb=" O ILE S 167 " (cutoff:3.500A) removed outlier: 6.724A 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: 4.196A pdb=" N LEU T 309 " --> pdb=" O TYR T 321 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N MET T 237 " --> pdb=" O GLU T 230 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLU T 230 " --> pdb=" O MET T 237 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE T 239 " --> pdb=" O VAL T 228 " (cutoff:3.500A) removed outlier: 5.937A 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 159 removed outlier: 3.684A pdb=" N ALA U 142 " --> pdb=" O GLY U 145 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE U 76 " --> pdb=" O ALA U 69 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ALA U 69 " --> pdb=" O ILE U 76 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE U 78 " --> pdb=" O ILE U 67 " (cutoff:3.500A) removed outlier: 5.993A 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: 4.091A pdb=" N VAL V 165 " --> pdb=" O LEU V 177 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE V 95 " --> pdb=" O THR V 92 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N CYS V 97 " --> pdb=" O LYS V 90 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS V 90 " --> pdb=" O CYS V 97 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ARG V 99 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.327A 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: 6.495A pdb=" N SER V 76 " --> pdb=" O VAL V 80 " (cutoff:3.500A) removed outlier: 5.755A 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 156 Processing sheet with id= BA, first strand: chain 'W' and resid 148 through 150 removed outlier: 5.559A pdb=" N CYS W 72 " --> pdb=" O TYR W 65 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TYR W 65 " --> pdb=" O CYS W 72 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLY W 74 " --> pdb=" O ILE W 63 " (cutoff:3.500A) removed outlier: 6.536A 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: 6.411A pdb=" N GLU W 51 " --> pdb=" O VAL W 55 " (cutoff:3.500A) removed outlier: 5.255A 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: 5.805A pdb=" N SER X 10 " --> pdb=" O ASP X 25 " (cutoff:3.500A) removed outlier: 3.968A 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: 3.544A pdb=" N ASN X 46 " --> pdb=" O ILE X 49 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR X 51 " --> pdb=" O VAL X 44 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL X 44 " --> pdb=" O TYR X 51 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU X 53 " --> pdb=" O LEU X 42 " (cutoff:3.500A) removed outlier: 6.319A 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: 6.291A pdb=" N GLU X 30 " --> pdb=" O THR X 34 " (cutoff:3.500A) removed outlier: 5.572A 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: 4.212A 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: 6.288A pdb=" N VAL Y 45 " --> pdb=" O GLN Y 38 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLN Y 38 " --> pdb=" O VAL Y 45 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N CYS Y 47 " --> pdb=" O ILE Y 36 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE Y 36 " --> pdb=" O CYS Y 47 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'Y' and resid 21 through 24 removed outlier: 3.511A pdb=" N THR Y 30 " --> pdb=" O ASN Y 22 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE Y 24 " --> pdb=" O LYS Y 28 " (cutoff:3.500A) removed outlier: 5.153A 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: 6.416A pdb=" N HIS Z 277 " --> pdb=" O LYS Z 285 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LYS Z 285 " --> pdb=" O HIS Z 277 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N HIS Z 279 " --> pdb=" O TRP Z 283 " (cutoff:3.500A) removed outlier: 4.863A 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: 3.841A 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: 6.188A pdb=" N THR Z 121 " --> pdb=" O ILE Z 125 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE Z 125 " --> pdb=" O THR Z 121 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'a' and resid 263 through 265 removed outlier: 5.191A 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: 3.577A pdb=" N GLU a 257 " --> pdb=" O SER a 249 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER a 249 " --> pdb=" O GLU a 257 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN a 234 " --> pdb=" O TYR a 250 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET a 177 " --> pdb=" O GLN a 170 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLN a 170 " --> pdb=" O MET a 177 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER a 179 " --> pdb=" O ILE a 168 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE a 168 " --> pdb=" O SER a 179 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'b' and resid 2 through 4 removed outlier: 6.475A pdb=" N TYR b 26 " --> pdb=" O ALA b 30 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ALA b 30 " --> pdb=" O TYR b 26 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'b' and resid 132 through 135 Processing sheet with id= BP, first strand: chain 'b' and resid 39 through 41 removed outlier: 3.500A pdb=" N SER b 45 " --> pdb=" O LEU b 41 " (cutoff:3.500A) 2468 hydrogen bonds defined for protein. 6963 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: 20.73 Time building geometry restraints manager: 19.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 10192 1.31 - 1.47: 17902 1.47 - 1.62: 21250 1.62 - 1.77: 25 1.77 - 1.92: 491 Bond restraints: 49860 Sorted by residual: bond pdb=" CE1 HIS b 44 " pdb=" NE2 HIS b 44 " ideal model delta sigma weight residual 1.321 1.434 -0.113 1.00e-02 1.00e+04 1.28e+02 bond pdb=" CE1 HIS N 44 " pdb=" NE2 HIS N 44 " ideal model delta sigma weight residual 1.321 1.433 -0.112 1.00e-02 1.00e+04 1.26e+02 bond pdb=" CE1 HIS I 145 " pdb=" NE2 HIS I 145 " ideal model delta sigma weight residual 1.321 1.410 -0.089 1.00e-02 1.00e+04 7.94e+01 bond pdb=" CE1 HIS W 145 " pdb=" NE2 HIS W 145 " ideal model delta sigma weight residual 1.321 1.410 -0.089 1.00e-02 1.00e+04 7.85e+01 bond pdb=" C10 VYW L4000 " pdb=" N3 VYW L4000 " ideal model delta sigma weight residual 1.484 1.310 0.174 2.00e-02 2.50e+03 7.55e+01 ... (remaining 49855 not shown) Histogram of bond angle deviations from ideal: 59.92 - 74.84: 6 74.84 - 89.75: 0 89.75 - 104.66: 1226 104.66 - 119.58: 43824 119.58 - 134.49: 22402 Bond angle restraints: 67458 Sorted by residual: angle pdb=" CA ASN L 137 " pdb=" CB ASN L 137 " pdb=" CG ASN L 137 " ideal model delta sigma weight residual 112.60 125.98 -13.38 1.00e+00 1.00e+00 1.79e+02 angle pdb=" CA ASN Z 137 " pdb=" CB ASN Z 137 " pdb=" CG ASN Z 137 " ideal model delta sigma weight residual 112.60 125.93 -13.33 1.00e+00 1.00e+00 1.78e+02 angle pdb=" C PHE a 270 " pdb=" CA PHE a 270 " pdb=" CB PHE a 270 " ideal model delta sigma weight residual 109.56 90.00 19.56 1.65e+00 3.67e-01 1.40e+02 angle pdb=" C PHE M 270 " pdb=" CA PHE M 270 " pdb=" CB PHE M 270 " ideal model delta sigma weight residual 109.56 90.14 19.42 1.65e+00 3.67e-01 1.39e+02 angle pdb=" CA ASP U 144 " pdb=" CB ASP U 144 " pdb=" CG ASP U 144 " ideal model delta sigma weight residual 112.60 122.64 -10.04 1.00e+00 1.00e+00 1.01e+02 ... (remaining 67453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 26323 18.05 - 36.11: 2629 36.11 - 54.16: 640 54.16 - 72.21: 230 72.21 - 90.27: 102 Dihedral angle restraints: 29924 sinusoidal: 11692 harmonic: 18232 Sorted by residual: dihedral pdb=" C PHE a 270 " pdb=" N PHE a 270 " pdb=" CA PHE a 270 " pdb=" CB PHE a 270 " ideal model delta harmonic sigma weight residual -122.60 -101.15 -21.45 0 2.50e+00 1.60e-01 7.36e+01 dihedral pdb=" C PHE M 270 " pdb=" N PHE M 270 " pdb=" CA PHE M 270 " pdb=" CB PHE M 270 " ideal model delta harmonic sigma weight residual -122.60 -101.23 -21.37 0 2.50e+00 1.60e-01 7.31e+01 dihedral pdb=" CA GLY T 289 " pdb=" C GLY T 289 " pdb=" N LYS T 290 " pdb=" CA LYS T 290 " ideal model delta harmonic sigma weight residual 180.00 139.21 40.79 0 5.00e+00 4.00e-02 6.66e+01 ... (remaining 29921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4510 0.079 - 0.158: 2279 0.158 - 0.238: 593 0.238 - 0.317: 110 0.317 - 0.396: 24 Chirality restraints: 7516 Sorted by residual: chirality pdb=" CA ARG P 210 " pdb=" N ARG P 210 " pdb=" C ARG P 210 " pdb=" CB ARG P 210 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CA SER S 196 " pdb=" N SER S 196 " pdb=" C SER S 196 " pdb=" CB SER S 196 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA SER E 196 " pdb=" N SER E 196 " pdb=" C SER E 196 " pdb=" CB SER E 196 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 7513 not shown) Planarity restraints: 8744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 106 " 0.926 9.50e-02 1.11e+02 4.15e-01 1.08e+02 pdb=" NE ARG L 106 " -0.041 2.00e-02 2.50e+03 pdb=" CZ ARG L 106 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG L 106 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG L 106 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Z 106 " -0.920 9.50e-02 1.11e+02 4.13e-01 1.07e+02 pdb=" NE ARG Z 106 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG Z 106 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG Z 106 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG Z 106 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 225 " -0.764 9.50e-02 1.11e+02 3.42e-01 7.14e+01 pdb=" NE ARG M 225 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG M 225 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG M 225 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG M 225 " -0.024 2.00e-02 2.50e+03 ... (remaining 8741 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 6550 2.72 - 3.27: 48202 3.27 - 3.81: 84994 3.81 - 4.36: 112423 4.36 - 4.90: 182540 Nonbonded interactions: 434709 Sorted by model distance: nonbonded pdb=" OG SER H 184 " pdb=" OD2 ASP H 221 " model vdw 2.180 2.440 nonbonded pdb=" OG SER V 184 " pdb=" OD2 ASP V 221 " model vdw 2.185 2.440 nonbonded pdb=" OD1 ASP Z 150 " pdb=" OH TYR a 223 " model vdw 2.227 2.440 nonbonded pdb=" OD1 ASP L 150 " pdb=" OH TYR M 223 " model vdw 2.231 2.440 nonbonded pdb=" NE2 GLN D 116 " pdb=" OD1 ASP E 184 " model vdw 2.233 2.520 ... (remaining 434704 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 8.360 Check model and map are aligned: 0.640 Set scattering table: 0.430 Process input model: 127.910 Find NCS groups from input model: 5.040 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:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 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 : 0.018 0.174 49860 Z= 1.179 Angle : 2.110 19.557 67458 Z= 1.389 Chirality : 0.096 0.396 7516 Planarity : 0.032 0.415 8744 Dihedral : 17.307 90.267 18276 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.01 % Favored : 95.41 % Rotamer: Outliers : 5.92 % Allowed : 8.93 % Favored : 85.14 % Cbeta Deviations : 1.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.77 (0.09), residues: 6256 helix: -2.40 (0.08), residues: 2330 sheet: -0.82 (0.12), residues: 1624 loop : -1.69 (0.11), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.017 TRP a 199 HIS 0.040 0.007 HIS P 69 PHE 0.078 0.015 PHE J 100 TYR 0.100 0.015 TYR P 116 ARG 0.049 0.005 ARG U 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 1179 time to evaluate : 5.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.7884 (tmm160) cc_final: 0.7439 (tmm160) REVERT: A 77 MET cc_start: 0.9013 (mmt) cc_final: 0.8617 (mmt) REVERT: A 141 ASP cc_start: 0.8943 (t70) cc_final: 0.8734 (t70) REVERT: A 150 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8387 (mmtt) REVERT: A 210 ILE cc_start: 0.8662 (pt) cc_final: 0.8393 (pt) REVERT: A 215 LYS cc_start: 0.8206 (mttt) cc_final: 0.7628 (ttpt) REVERT: A 228 ASN cc_start: 0.8130 (t0) cc_final: 0.7904 (t0) REVERT: B 16 LYS cc_start: 0.8798 (mttt) cc_final: 0.8410 (mmpt) REVERT: B 90 LYS cc_start: 0.9011 (mtpt) cc_final: 0.8727 (mtmt) REVERT: B 100 ASN cc_start: 0.8950 (t0) cc_final: 0.8698 (t0) REVERT: B 140 ASN cc_start: 0.8561 (m-40) cc_final: 0.8314 (m110) REVERT: B 154 TRP cc_start: 0.8589 (m100) cc_final: 0.7930 (m-90) REVERT: B 169 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7614 (mtmm) REVERT: B 175 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7557 (mtp-110) REVERT: B 181 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7195 (pp20) REVERT: B 183 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7046 (tp30) REVERT: B 202 THR cc_start: 0.7812 (p) cc_final: 0.7381 (p) REVERT: B 204 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7957 (mp0) REVERT: B 205 ASN cc_start: 0.8534 (p0) cc_final: 0.7715 (p0) REVERT: B 214 ASN cc_start: 0.8567 (p0) cc_final: 0.8302 (m110) REVERT: C 17 ARG cc_start: 0.8264 (mtp180) cc_final: 0.8045 (mtm180) REVERT: C 26 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8099 (mt-10) REVERT: C 50 MET cc_start: 0.7411 (ptm) cc_final: 0.7157 (ppp) REVERT: C 71 MET cc_start: 0.8963 (mmt) cc_final: 0.8674 (mmt) REVERT: C 111 MET cc_start: 0.9192 (ttt) cc_final: 0.8779 (ttt) REVERT: C 180 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8555 (mt) REVERT: C 182 LYS cc_start: 0.7800 (ttmt) cc_final: 0.7432 (mmtp) REVERT: C 183 LYS cc_start: 0.7756 (ttpt) cc_final: 0.7510 (tttp) REVERT: C 192 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7449 (mp0) REVERT: C 204 LYS cc_start: 0.8185 (tptm) cc_final: 0.7706 (tttm) REVERT: C 206 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8152 (ptm) REVERT: C 221 MET cc_start: 0.9038 (tpp) cc_final: 0.8803 (tpp) REVERT: C 222 ARG cc_start: 0.8696 (ptt-90) cc_final: 0.8048 (ptp-170) REVERT: C 255 LYS cc_start: 0.7377 (tttt) cc_final: 0.7070 (tptp) REVERT: D 54 GLN cc_start: 0.8333 (pt0) cc_final: 0.7578 (mm-40) REVERT: D 59 ILE cc_start: 0.6368 (OUTLIER) cc_final: 0.5806 (pp) REVERT: D 103 ASP cc_start: 0.8791 (m-30) cc_final: 0.8558 (m-30) REVERT: D 141 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7805 (mmmt) REVERT: D 163 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8644 (ptt90) REVERT: D 172 MET cc_start: 0.8944 (mtm) cc_final: 0.8674 (mtm) REVERT: D 177 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7216 (mmpt) REVERT: D 180 MET cc_start: 0.8282 (mtm) cc_final: 0.7901 (mtm) REVERT: D 196 VAL cc_start: 0.8006 (m) cc_final: 0.7784 (m) REVERT: D 228 GLU cc_start: 0.6117 (tt0) cc_final: 0.5542 (tt0) REVERT: D 230 GLU cc_start: 0.5970 (tt0) cc_final: 0.5430 (tp30) REVERT: D 232 GLU cc_start: 0.6149 (tt0) cc_final: 0.5824 (tm-30) REVERT: E 110 ARG cc_start: 0.6222 (mtm-85) cc_final: 0.6004 (mtm180) REVERT: E 120 ARG cc_start: 0.8645 (mtt90) cc_final: 0.8409 (mtm-85) REVERT: E 141 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7756 (ttp80) REVERT: E 144 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7462 (mt-10) REVERT: E 171 ASP cc_start: 0.8929 (t0) cc_final: 0.8727 (t0) REVERT: E 233 MET cc_start: 0.7231 (mmt) cc_final: 0.6849 (mmt) REVERT: E 248 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7221 (tt0) REVERT: E 264 ARG cc_start: 0.8514 (ttp-110) cc_final: 0.8065 (ttm110) REVERT: E 278 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7306 (mt0) REVERT: E 282 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7582 (p) REVERT: E 289 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7650 (ptp) REVERT: E 290 THR cc_start: 0.8134 (p) cc_final: 0.7616 (t) REVERT: E 293 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6547 (mm-30) REVERT: E 313 GLU cc_start: 0.7573 (mp0) cc_final: 0.7239 (mp0) REVERT: E 316 GLU cc_start: 0.8577 (tt0) cc_final: 0.8367 (mt-10) REVERT: E 342 MET cc_start: 0.4126 (ttm) cc_final: 0.3760 (tpt) REVERT: F 169 GLU cc_start: 0.7180 (tt0) cc_final: 0.6943 (mp0) REVERT: F 190 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8285 (m110) REVERT: F 304 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7949 (mtm-85) REVERT: G 29 LYS cc_start: 0.8617 (mmtp) cc_final: 0.8408 (mttm) REVERT: G 33 ASN cc_start: 0.8580 (m-40) cc_final: 0.8339 (m-40) REVERT: G 43 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7550 (mmmm) REVERT: G 51 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8020 (pp20) REVERT: G 61 LYS cc_start: 0.7537 (mttt) cc_final: 0.7179 (mmtt) REVERT: G 180 ASP cc_start: 0.7895 (t0) cc_final: 0.7573 (t70) REVERT: G 184 LEU cc_start: 0.7796 (tp) cc_final: 0.7571 (tp) REVERT: H 123 ASP cc_start: 0.8843 (t70) cc_final: 0.8627 (t70) REVERT: H 137 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: H 203 LYS cc_start: 0.8684 (tttt) cc_final: 0.8432 (tttp) REVERT: I 59 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7856 (mtm-85) REVERT: I 71 MET cc_start: 0.8989 (mmm) cc_final: 0.8776 (mmm) REVERT: I 78 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8657 (t) REVERT: I 82 GLU cc_start: 0.8611 (tp30) cc_final: 0.8384 (tm-30) REVERT: I 120 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8224 (mm110) REVERT: I 175 MET cc_start: 0.9114 (mtm) cc_final: 0.8890 (mtm) REVERT: I 179 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8341 (mt-10) REVERT: I 213 GLU cc_start: 0.8439 (tt0) cc_final: 0.8195 (mp0) REVERT: I 244 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7087 (tm-30) REVERT: J 3 ILE cc_start: 0.8749 (mt) cc_final: 0.8232 (tp) REVERT: J 4 MET cc_start: 0.8579 (mmm) cc_final: 0.8337 (mmt) REVERT: J 12 MET cc_start: 0.8998 (tmm) cc_final: 0.8712 (tmm) REVERT: J 41 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8704 (mmtm) REVERT: J 66 LYS cc_start: 0.9234 (mtpp) cc_final: 0.9007 (mtpp) REVERT: J 68 GLN cc_start: 0.8874 (tt0) cc_final: 0.8616 (tt0) REVERT: J 92 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8907 (m) REVERT: J 97 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8625 (mt-10) REVERT: J 118 GLU cc_start: 0.8332 (tt0) cc_final: 0.7926 (mm-30) REVERT: J 158 MET cc_start: 0.8848 (mtp) cc_final: 0.8201 (mtm) REVERT: J 171 MET cc_start: 0.9081 (tpp) cc_final: 0.8771 (tpt) REVERT: J 188 MET cc_start: 0.9097 (mtp) cc_final: 0.8770 (mtp) REVERT: K 1 MET cc_start: 0.7162 (mmm) cc_final: 0.6712 (mtm) REVERT: K 3 GLU cc_start: 0.8114 (mp0) cc_final: 0.7829 (pt0) REVERT: K 31 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7755 (OUTLIER) REVERT: K 50 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8262 (mp0) REVERT: K 70 MET cc_start: 0.8648 (mmp) cc_final: 0.8370 (mmt) REVERT: K 125 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8667 (mm110) REVERT: K 159 ARG cc_start: 0.8681 (mtm110) cc_final: 0.8413 (mtm-85) REVERT: K 173 LYS cc_start: 0.8845 (mttt) cc_final: 0.8640 (mttp) REVERT: K 180 ARG cc_start: 0.8702 (ttm110) cc_final: 0.8327 (ttp-170) REVERT: K 206 HIS cc_start: 0.7938 (p90) cc_final: 0.7693 (p90) REVERT: L 123 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: L 131 MET cc_start: 0.8268 (mtp) cc_final: 0.8030 (tpt) REVERT: L 134 LEU cc_start: 0.8507 (tp) cc_final: 0.8249 (mt) REVERT: L 137 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.6923 (t0) REVERT: L 139 TYR cc_start: 0.7776 (m-80) cc_final: 0.7284 (m-80) REVERT: L 160 MET cc_start: 0.9273 (ttp) cc_final: 0.9013 (ttp) REVERT: L 172 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.8092 (mtm110) REVERT: L 205 GLN cc_start: 0.8154 (pm20) cc_final: 0.7795 (pm20) REVERT: L 244 LYS cc_start: 0.8385 (mttt) cc_final: 0.8109 (mmtp) REVERT: M 170 GLN cc_start: 0.8954 (tt0) cc_final: 0.8726 (tt0) REVERT: M 177 MET cc_start: 0.9120 (ptm) cc_final: 0.8649 (ptm) REVERT: M 201 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8264 (mmmt) REVERT: M 257 GLU cc_start: 0.8408 (pt0) cc_final: 0.8118 (pt0) REVERT: M 281 ARG cc_start: 0.8613 (mtp85) cc_final: 0.8410 (mtp85) REVERT: M 292 MET cc_start: 0.8077 (mtm) cc_final: 0.7716 (ttm) REVERT: M 330 GLN cc_start: 0.8656 (mt0) cc_final: 0.8274 (mm-40) REVERT: M 332 GLU cc_start: 0.8457 (tt0) cc_final: 0.8152 (tt0) REVERT: N 1 MET cc_start: 0.7704 (mmm) cc_final: 0.7428 (mmm) REVERT: N 13 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8516 (mtpm) REVERT: N 39 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8261 (ttm170) REVERT: N 59 MET cc_start: 0.8982 (tpp) cc_final: 0.8768 (tpt) REVERT: N 64 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8004 (tp30) REVERT: N 106 MET cc_start: 0.8848 (mtt) cc_final: 0.8509 (mtt) REVERT: N 135 THR cc_start: 0.9291 (p) cc_final: 0.9024 (p) REVERT: N 151 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7659 (mt-10) REVERT: N 164 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8478 (ttp80) REVERT: N 203 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8219 (mp0) REVERT: N 207 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8150 (mm-30) REVERT: O 56 ARG cc_start: 0.7881 (tmm160) cc_final: 0.7441 (tmm160) REVERT: O 77 MET cc_start: 0.9006 (mmt) cc_final: 0.8616 (mmt) REVERT: O 141 ASP cc_start: 0.8945 (t70) cc_final: 0.8736 (t70) REVERT: O 150 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8407 (mmtt) REVERT: O 210 ILE cc_start: 0.8653 (pt) cc_final: 0.8387 (pt) REVERT: O 214 VAL cc_start: 0.8352 (m) cc_final: 0.8141 (p) REVERT: O 215 LYS cc_start: 0.8200 (mttt) cc_final: 0.7602 (ttpt) REVERT: O 228 ASN cc_start: 0.8243 (t0) cc_final: 0.8016 (t0) REVERT: P 16 LYS cc_start: 0.8805 (mttt) cc_final: 0.8415 (mmpt) REVERT: P 61 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: P 90 LYS cc_start: 0.9011 (mtpt) cc_final: 0.8724 (mtmt) REVERT: P 100 ASN cc_start: 0.8966 (t0) cc_final: 0.8717 (t0) REVERT: P 140 ASN cc_start: 0.8545 (m-40) cc_final: 0.8281 (m110) REVERT: P 154 TRP cc_start: 0.8598 (m100) cc_final: 0.7943 (m-90) REVERT: P 169 LYS cc_start: 0.7902 (mtmt) cc_final: 0.7624 (mtmm) REVERT: P 175 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7587 (mtp-110) REVERT: P 180 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7218 (ttp) REVERT: P 181 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7396 (tm-30) REVERT: P 183 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7154 (tp30) REVERT: P 202 THR cc_start: 0.7812 (p) cc_final: 0.7374 (p) REVERT: P 204 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7948 (mp0) REVERT: P 205 ASN cc_start: 0.8564 (p0) cc_final: 0.7758 (p0) REVERT: P 214 ASN cc_start: 0.8558 (p0) cc_final: 0.8307 (m110) REVERT: Q 4 ARG cc_start: 0.8515 (mtp-110) cc_final: 0.7968 (mtm110) REVERT: Q 17 ARG cc_start: 0.8259 (mtp180) cc_final: 0.8043 (mtm180) REVERT: Q 26 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8089 (mt-10) REVERT: Q 50 MET cc_start: 0.7405 (ptm) cc_final: 0.7138 (ppp) REVERT: Q 71 MET cc_start: 0.8966 (mmt) cc_final: 0.8672 (mmt) REVERT: Q 111 MET cc_start: 0.9183 (ttt) cc_final: 0.8792 (ttt) REVERT: Q 180 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8557 (mt) REVERT: Q 182 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7552 (mmtp) REVERT: Q 183 LYS cc_start: 0.7707 (ttpt) cc_final: 0.7473 (tttp) REVERT: Q 192 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7442 (mp0) REVERT: Q 204 LYS cc_start: 0.8183 (tptm) cc_final: 0.7706 (tttm) REVERT: Q 206 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8168 (ptm) REVERT: Q 221 MET cc_start: 0.9043 (tpp) cc_final: 0.8809 (tpp) REVERT: Q 222 ARG cc_start: 0.8701 (ptt-90) cc_final: 0.8048 (ptp-170) REVERT: Q 255 LYS cc_start: 0.7372 (tttt) cc_final: 0.7069 (tptp) REVERT: R 54 GLN cc_start: 0.8332 (pt0) cc_final: 0.7578 (mm-40) REVERT: R 59 ILE cc_start: 0.6478 (OUTLIER) cc_final: 0.5905 (pp) REVERT: R 103 ASP cc_start: 0.8802 (m-30) cc_final: 0.8560 (m-30) REVERT: R 141 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7795 (mmmt) REVERT: R 163 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8647 (ptt90) REVERT: R 172 MET cc_start: 0.8949 (mtm) cc_final: 0.8684 (mtm) REVERT: R 177 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7214 (mmpt) REVERT: R 180 MET cc_start: 0.8264 (mtm) cc_final: 0.7864 (mtm) REVERT: R 196 VAL cc_start: 0.8024 (m) cc_final: 0.7792 (m) REVERT: R 228 GLU cc_start: 0.6147 (tt0) cc_final: 0.5582 (tt0) REVERT: R 230 GLU cc_start: 0.5974 (tt0) cc_final: 0.5495 (tp30) REVERT: R 232 GLU cc_start: 0.6132 (tt0) cc_final: 0.5824 (tm-30) REVERT: S 110 ARG cc_start: 0.6206 (mtm-85) cc_final: 0.5992 (mtm180) REVERT: S 120 ARG cc_start: 0.8647 (mtt90) cc_final: 0.8408 (mtm-85) REVERT: S 141 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7758 (ttp80) REVERT: S 144 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7465 (mt-10) REVERT: S 153 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7912 (ttm170) REVERT: S 171 ASP cc_start: 0.8933 (t0) cc_final: 0.8727 (t0) REVERT: S 233 MET cc_start: 0.7204 (mmt) cc_final: 0.6828 (mmt) REVERT: S 248 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7206 (tt0) REVERT: S 264 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.8052 (ttm110) REVERT: S 278 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7322 (mt0) REVERT: S 282 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7582 (p) REVERT: S 289 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7661 (ptp) REVERT: S 290 THR cc_start: 0.8134 (p) cc_final: 0.7618 (t) REVERT: S 293 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6555 (mm-30) REVERT: S 313 GLU cc_start: 0.7573 (mp0) cc_final: 0.7291 (mp0) REVERT: S 342 MET cc_start: 0.4104 (ttm) cc_final: 0.3741 (tpt) REVERT: T 169 GLU cc_start: 0.7190 (tt0) cc_final: 0.6960 (mp0) REVERT: T 190 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8289 (m110) REVERT: T 304 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7947 (mtm-85) REVERT: T 371 ASN cc_start: 0.8526 (p0) cc_final: 0.8325 (p0) REVERT: U 29 LYS cc_start: 0.8618 (mmtp) cc_final: 0.8408 (mttm) REVERT: U 33 ASN cc_start: 0.8576 (m-40) cc_final: 0.8329 (m-40) REVERT: U 43 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7568 (mmmm) REVERT: U 51 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8036 (pp20) REVERT: U 61 LYS cc_start: 0.7545 (mttt) cc_final: 0.7193 (mmtt) REVERT: U 180 ASP cc_start: 0.7918 (t0) cc_final: 0.7543 (t70) REVERT: U 184 LEU cc_start: 0.7807 (tp) cc_final: 0.7581 (tp) REVERT: U 202 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7857 (t70) REVERT: U 221 ASP cc_start: 0.8280 (t0) cc_final: 0.8068 (t0) REVERT: V 123 ASP cc_start: 0.8842 (t70) cc_final: 0.8625 (t70) REVERT: V 137 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.8318 (m-80) REVERT: V 203 LYS cc_start: 0.8679 (tttt) cc_final: 0.8438 (tttp) REVERT: V 280 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.8550 (p) REVERT: W 58 LYS cc_start: 0.8502 (mtmt) cc_final: 0.8267 (mtmt) REVERT: W 59 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7831 (mtm-85) REVERT: W 71 MET cc_start: 0.8979 (mmm) cc_final: 0.8758 (mmm) REVERT: W 78 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8644 (t) REVERT: W 82 GLU cc_start: 0.8606 (tp30) cc_final: 0.8390 (tm-30) REVERT: W 120 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8221 (mm110) REVERT: W 175 MET cc_start: 0.9127 (mtm) cc_final: 0.8900 (mtm) REVERT: W 179 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8368 (mt-10) REVERT: W 213 GLU cc_start: 0.8438 (tt0) cc_final: 0.8202 (mp0) REVERT: W 244 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7121 (tm-30) REVERT: X 3 ILE cc_start: 0.8723 (mt) cc_final: 0.8205 (tp) REVERT: X 12 MET cc_start: 0.8997 (tmm) cc_final: 0.8713 (tmm) REVERT: X 31 GLN cc_start: 0.8623 (mt0) cc_final: 0.8414 (mt0) REVERT: X 41 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8705 (mmtm) REVERT: X 66 LYS cc_start: 0.9229 (mtpp) cc_final: 0.9003 (mtpp) REVERT: X 68 GLN cc_start: 0.8877 (tt0) cc_final: 0.8617 (tt0) REVERT: X 92 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8888 (m) REVERT: X 97 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8622 (mt-10) REVERT: X 118 GLU cc_start: 0.8325 (tt0) cc_final: 0.7924 (mm-30) REVERT: X 158 MET cc_start: 0.8853 (mtp) cc_final: 0.8215 (mtm) REVERT: X 171 MET cc_start: 0.9079 (tpp) cc_final: 0.8769 (tpt) REVERT: X 188 MET cc_start: 0.9092 (mtp) cc_final: 0.8771 (mtp) REVERT: Y 1 MET cc_start: 0.7129 (mmm) cc_final: 0.6699 (mtm) REVERT: Y 3 GLU cc_start: 0.8107 (mp0) cc_final: 0.7826 (pt0) REVERT: Y 31 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: Y 50 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8271 (mp0) REVERT: Y 70 MET cc_start: 0.8656 (mmp) cc_final: 0.8382 (mmt) REVERT: Y 125 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8674 (mm110) REVERT: Y 159 ARG cc_start: 0.8677 (mtm110) cc_final: 0.8420 (mtm-85) REVERT: Y 164 GLN cc_start: 0.8484 (tp40) cc_final: 0.8279 (tp40) REVERT: Y 173 LYS cc_start: 0.8837 (mttt) cc_final: 0.8631 (mttp) REVERT: Y 180 ARG cc_start: 0.8704 (ttm110) cc_final: 0.8327 (ttp-170) REVERT: Y 206 HIS cc_start: 0.7927 (p90) cc_final: 0.7685 (p90) REVERT: Z 123 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: Z 131 MET cc_start: 0.8265 (mtp) cc_final: 0.8027 (tpt) REVERT: Z 134 LEU cc_start: 0.8506 (tp) cc_final: 0.8248 (mt) REVERT: Z 137 ASN cc_start: 0.7301 (OUTLIER) cc_final: 0.6928 (t0) REVERT: Z 139 TYR cc_start: 0.7760 (m-80) cc_final: 0.7267 (m-80) REVERT: Z 172 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.8101 (mtm110) REVERT: Z 205 GLN cc_start: 0.8117 (pm20) cc_final: 0.7774 (pm20) REVERT: Z 244 LYS cc_start: 0.8411 (mttt) cc_final: 0.8130 (mmtp) REVERT: a 167 LYS cc_start: 0.8851 (mttp) cc_final: 0.8592 (mttm) REVERT: a 177 MET cc_start: 0.9122 (ptm) cc_final: 0.8646 (ptm) REVERT: a 201 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8254 (mmmt) REVERT: a 257 GLU cc_start: 0.8434 (pt0) cc_final: 0.8138 (pt0) REVERT: a 281 ARG cc_start: 0.8610 (mtp85) cc_final: 0.8410 (mtp85) REVERT: a 292 MET cc_start: 0.8058 (mtm) cc_final: 0.7647 (ttm) REVERT: a 330 GLN cc_start: 0.8644 (mt0) cc_final: 0.8260 (mm-40) REVERT: a 331 GLN cc_start: 0.8093 (mt0) cc_final: 0.7745 (mt0) REVERT: a 332 GLU cc_start: 0.8457 (tt0) cc_final: 0.8134 (tt0) REVERT: b 1 MET cc_start: 0.7721 (mmm) cc_final: 0.7431 (mmm) REVERT: b 13 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8516 (mtpm) REVERT: b 39 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8262 (ttm170) REVERT: b 59 MET cc_start: 0.8985 (tpp) cc_final: 0.8784 (tpt) REVERT: b 64 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8021 (tp30) REVERT: b 106 MET cc_start: 0.8853 (mtt) cc_final: 0.8508 (mtt) REVERT: b 135 THR cc_start: 0.9303 (p) cc_final: 0.9049 (p) REVERT: b 164 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8452 (ttp80) REVERT: b 203 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8216 (mp0) REVERT: b 207 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8247 (mm-30) outliers start: 309 outliers final: 81 residues processed: 1382 average time/residue: 1.8424 time to fit residues: 3098.0953 Evaluate side-chains 986 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 850 time to evaluate : 5.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain D residue 12 PRO Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 304 ARG Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 173 SER Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 224 SER Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain M residue 201 LYS Chi-restraints excluded: chain M residue 219 SER Chi-restraints excluded: chain M residue 333 SER Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 144 PRO Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 11 THR Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 61 GLN Chi-restraints excluded: chain P residue 175 ARG Chi-restraints excluded: chain P residue 180 MET Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 119 ILE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain Q residue 206 MET Chi-restraints excluded: chain Q residue 233 LEU Chi-restraints excluded: chain Q residue 252 SER Chi-restraints excluded: chain R residue 12 PRO Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 163 ARG Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain S residue 141 ARG Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 278 GLN Chi-restraints excluded: chain S residue 282 THR Chi-restraints excluded: chain S residue 289 MET Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 304 ARG Chi-restraints excluded: chain T residue 362 SER Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 51 GLU Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 195 SER Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain V residue 76 SER Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 149 SER Chi-restraints excluded: chain V residue 173 SER Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 224 SER Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain V residue 280 SER Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain X residue 41 LYS Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 116 THR Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain Z residue 137 ASN Chi-restraints excluded: chain Z residue 144 LEU Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 284 THR Chi-restraints excluded: chain a residue 201 LYS Chi-restraints excluded: chain a residue 219 SER Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 64 GLU Chi-restraints excluded: chain b residue 144 PRO Chi-restraints excluded: chain b residue 164 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 521 optimal weight: 0.8980 chunk 468 optimal weight: 0.8980 chunk 259 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 chunk 315 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 484 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 294 optimal weight: 0.9980 chunk 360 optimal weight: 5.9990 chunk 561 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 207 GLN A 236 ASN B 107 GLN B 200 GLN C 239 HIS C 257 HIS D 23 GLN E 222 GLN E 255 GLN E 262 HIS E 288 ASN F 331 GLN ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 HIS I 201 GLN J 31 GLN J 65 ASN K 72 GLN K 102 GLN K 186 ASN L 108 ASN L 291 GLN N 66 ASN N 70 GLN N 148 GLN N 205 HIS O 89 GLN O 207 GLN P 107 GLN P 200 GLN Q 239 HIS Q 257 HIS R 23 GLN S 222 GLN S 255 GLN S 262 HIS S 288 ASN T 331 GLN ** V 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 115 HIS W 201 GLN X 65 ASN Y 72 GLN Y 102 GLN Y 164 GLN Y 186 ASN Z 108 ASN Z 291 GLN a 280 ASN b 66 ASN b 70 GLN b 148 GLN b 205 HIS Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 49860 Z= 0.201 Angle : 0.608 7.454 67458 Z= 0.328 Chirality : 0.044 0.159 7516 Planarity : 0.004 0.059 8744 Dihedral : 7.852 65.280 7225 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.71 % Favored : 98.23 % Rotamer: Outliers : 2.74 % Allowed : 14.40 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -0.15 (0.10), residues: 6256 helix: 0.52 (0.10), residues: 2310 sheet: 0.16 (0.13), residues: 1556 loop : -0.76 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP V 245 HIS 0.006 0.001 HIS L 277 PHE 0.016 0.002 PHE B 64 TYR 0.021 0.002 TYR V 190 ARG 0.006 0.001 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 990 time to evaluate : 6.254 Fit side-chains REVERT: A 56 ARG cc_start: 0.7696 (tmm160) cc_final: 0.7379 (tmm160) REVERT: A 140 MET cc_start: 0.8934 (mmm) cc_final: 0.8566 (mmt) REVERT: A 150 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8181 (mmtp) REVERT: A 215 LYS cc_start: 0.8028 (mttt) cc_final: 0.7653 (mmtt) REVERT: B 16 LYS cc_start: 0.8592 (mttt) cc_final: 0.8098 (mmpt) REVERT: B 21 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8095 (mt-10) REVERT: B 90 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8578 (mtmt) REVERT: B 140 ASN cc_start: 0.8369 (m-40) cc_final: 0.8123 (m110) REVERT: B 166 PRO cc_start: 0.8517 (Cg_exo) cc_final: 0.8315 (Cg_endo) REVERT: B 169 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7494 (mtmm) REVERT: B 175 ARG cc_start: 0.7854 (mtp85) cc_final: 0.7575 (mtp-110) REVERT: B 183 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7089 (tp30) REVERT: B 205 ASN cc_start: 0.8397 (p0) cc_final: 0.7965 (p0) REVERT: B 214 ASN cc_start: 0.8381 (p0) cc_final: 0.8150 (m110) REVERT: B 215 ARG cc_start: 0.8461 (ptt-90) cc_final: 0.8138 (ptt-90) REVERT: C 50 MET cc_start: 0.7423 (ptm) cc_final: 0.7142 (ppp) REVERT: C 180 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8391 (mt) REVERT: C 204 LYS cc_start: 0.8385 (tptm) cc_final: 0.7851 (tttm) REVERT: C 245 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8157 (ttt90) REVERT: C 266 GLU cc_start: 0.5656 (mt-10) cc_final: 0.5345 (mm-30) REVERT: D 54 GLN cc_start: 0.8265 (pt0) cc_final: 0.7355 (mm-40) REVERT: D 141 LYS cc_start: 0.8036 (ttmt) cc_final: 0.7728 (mmmt) REVERT: D 180 MET cc_start: 0.8162 (mtm) cc_final: 0.7913 (mtm) REVERT: D 224 LYS cc_start: 0.6805 (mttt) cc_final: 0.6534 (ttpt) REVERT: D 228 GLU cc_start: 0.6072 (tt0) cc_final: 0.5814 (tt0) REVERT: D 232 GLU cc_start: 0.6177 (tt0) cc_final: 0.5857 (tm-30) REVERT: E 164 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7839 (mmm) REVERT: E 233 MET cc_start: 0.6795 (mmt) cc_final: 0.6444 (mmt) REVERT: E 265 TYR cc_start: 0.8459 (m-80) cc_final: 0.8077 (m-80) REVERT: E 278 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7117 (mt0) REVERT: E 282 THR cc_start: 0.7736 (OUTLIER) cc_final: 0.7248 (p) REVERT: E 289 MET cc_start: 0.8021 (ptm) cc_final: 0.7529 (ptp) REVERT: E 313 GLU cc_start: 0.7810 (mp0) cc_final: 0.7446 (mp0) REVERT: E 339 MET cc_start: 0.6276 (mtm) cc_final: 0.5953 (mmm) REVERT: E 342 MET cc_start: 0.4002 (ttm) cc_final: 0.3336 (tmt) REVERT: F 190 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.8065 (m110) REVERT: F 205 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7789 (tttm) REVERT: F 304 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7892 (mtm-85) REVERT: G 33 ASN cc_start: 0.8459 (m-40) cc_final: 0.8235 (m-40) REVERT: G 43 LYS cc_start: 0.7672 (pttt) cc_final: 0.7467 (mmmt) REVERT: G 61 LYS cc_start: 0.7547 (mttt) cc_final: 0.7263 (mmtt) REVERT: G 180 ASP cc_start: 0.7796 (t0) cc_final: 0.7394 (t70) REVERT: H 137 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8743 (m-80) REVERT: H 139 LYS cc_start: 0.8491 (tppp) cc_final: 0.8131 (tttt) REVERT: I 61 ARG cc_start: 0.8050 (mmt180) cc_final: 0.7794 (mmm-85) REVERT: I 78 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8369 (t) REVERT: I 82 GLU cc_start: 0.8378 (tp30) cc_final: 0.8091 (tm-30) REVERT: I 120 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8184 (mm110) REVERT: I 213 GLU cc_start: 0.8384 (tt0) cc_final: 0.8172 (mp0) REVERT: I 244 GLU cc_start: 0.8066 (mt-10) cc_final: 0.6980 (tm-30) REVERT: I 246 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7025 (ttm170) REVERT: J 4 MET cc_start: 0.8720 (mmm) cc_final: 0.8410 (mmt) REVERT: J 12 MET cc_start: 0.8929 (tmm) cc_final: 0.8641 (tmm) REVERT: J 31 GLN cc_start: 0.8557 (mt0) cc_final: 0.8191 (mt0) REVERT: J 66 LYS cc_start: 0.9100 (mtpp) cc_final: 0.8865 (mtpp) REVERT: J 118 GLU cc_start: 0.8184 (tt0) cc_final: 0.7722 (mm-30) REVERT: J 158 MET cc_start: 0.8476 (mtp) cc_final: 0.8233 (mtm) REVERT: J 171 MET cc_start: 0.8986 (tpp) cc_final: 0.8603 (tpp) REVERT: K 1 MET cc_start: 0.7076 (mmm) cc_final: 0.6723 (mmm) REVERT: K 72 GLN cc_start: 0.8120 (mt0) cc_final: 0.7733 (mt0) REVERT: K 76 HIS cc_start: 0.7383 (m-70) cc_final: 0.6703 (p-80) REVERT: K 116 GLU cc_start: 0.7332 (pm20) cc_final: 0.6990 (pp20) REVERT: K 125 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8470 (mm110) REVERT: K 180 ARG cc_start: 0.8608 (ttm110) cc_final: 0.8270 (ttp-170) REVERT: K 206 HIS cc_start: 0.7840 (p90) cc_final: 0.7562 (p90) REVERT: L 123 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: L 172 ARG cc_start: 0.8426 (mtm-85) cc_final: 0.8039 (mtm110) REVERT: L 205 GLN cc_start: 0.7974 (pm20) cc_final: 0.7572 (pm20) REVERT: L 240 THR cc_start: 0.8030 (m) cc_final: 0.7699 (t) REVERT: L 244 LYS cc_start: 0.8123 (mttt) cc_final: 0.7822 (mmtp) REVERT: L 249 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7696 (mp0) REVERT: M 170 GLN cc_start: 0.8870 (tt0) cc_final: 0.8521 (tt0) REVERT: M 201 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8086 (ttmm) REVERT: M 326 LYS cc_start: 0.7716 (pttp) cc_final: 0.7321 (ptmt) REVERT: M 331 GLN cc_start: 0.7883 (tt0) cc_final: 0.7460 (mt0) REVERT: M 332 GLU cc_start: 0.8377 (tt0) cc_final: 0.8071 (tt0) REVERT: N 13 LYS cc_start: 0.8284 (mtmt) cc_final: 0.8038 (mtpm) REVERT: N 64 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7981 (tp30) REVERT: N 130 ASP cc_start: 0.8103 (t70) cc_final: 0.7902 (t70) REVERT: N 163 MET cc_start: 0.8731 (tpp) cc_final: 0.8456 (tpp) REVERT: O 56 ARG cc_start: 0.7697 (tmm160) cc_final: 0.7381 (tmm160) REVERT: O 140 MET cc_start: 0.8937 (mmm) cc_final: 0.8564 (mmt) REVERT: O 150 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8187 (mmtp) REVERT: O 215 LYS cc_start: 0.8029 (mttt) cc_final: 0.7489 (ttpt) REVERT: P 16 LYS cc_start: 0.8590 (mttt) cc_final: 0.8097 (mmpt) REVERT: P 21 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8081 (mt-10) REVERT: P 90 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8576 (mtmt) REVERT: P 140 ASN cc_start: 0.8357 (m-40) cc_final: 0.8106 (m110) REVERT: P 166 PRO cc_start: 0.8582 (Cg_exo) cc_final: 0.8354 (Cg_endo) REVERT: P 169 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7455 (mtmm) REVERT: P 175 ARG cc_start: 0.7752 (mmm160) cc_final: 0.7087 (mmt180) REVERT: P 183 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7037 (tp30) REVERT: P 205 ASN cc_start: 0.8380 (p0) cc_final: 0.7959 (p0) REVERT: P 214 ASN cc_start: 0.8380 (p0) cc_final: 0.8152 (m110) REVERT: P 215 ARG cc_start: 0.8467 (ptt-90) cc_final: 0.8149 (ptt-90) REVERT: Q 50 MET cc_start: 0.7421 (ptm) cc_final: 0.7139 (ppp) REVERT: Q 180 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8386 (mt) REVERT: Q 204 LYS cc_start: 0.8378 (tptm) cc_final: 0.7853 (tttm) REVERT: Q 245 ARG cc_start: 0.8410 (ttp80) cc_final: 0.8154 (ttt90) REVERT: R 54 GLN cc_start: 0.8238 (pt0) cc_final: 0.7343 (mm-40) REVERT: R 180 MET cc_start: 0.8168 (mtm) cc_final: 0.7937 (mtm) REVERT: R 224 LYS cc_start: 0.6801 (mttt) cc_final: 0.6534 (ttpt) REVERT: R 228 GLU cc_start: 0.6092 (tt0) cc_final: 0.5838 (tt0) REVERT: R 232 GLU cc_start: 0.6175 (tt0) cc_final: 0.5884 (tm-30) REVERT: S 233 MET cc_start: 0.6784 (mmt) cc_final: 0.6439 (mmt) REVERT: S 248 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7115 (tt0) REVERT: S 265 TYR cc_start: 0.8461 (m-80) cc_final: 0.8085 (m-80) REVERT: S 278 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7098 (mt0) REVERT: S 282 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7235 (p) REVERT: S 289 MET cc_start: 0.8003 (ptm) cc_final: 0.7601 (ptp) REVERT: S 313 GLU cc_start: 0.7867 (mp0) cc_final: 0.7471 (mp0) REVERT: S 339 MET cc_start: 0.6294 (mtm) cc_final: 0.5963 (mmm) REVERT: S 342 MET cc_start: 0.3978 (ttm) cc_final: 0.3318 (tmt) REVERT: T 190 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.8063 (m110) REVERT: T 205 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7779 (tttm) REVERT: T 304 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7888 (mtm-85) REVERT: U 33 ASN cc_start: 0.8471 (m-40) cc_final: 0.8247 (m-40) REVERT: U 61 LYS cc_start: 0.7549 (mttt) cc_final: 0.7275 (mmtt) REVERT: U 180 ASP cc_start: 0.7797 (t0) cc_final: 0.7381 (t70) REVERT: V 137 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8744 (m-80) REVERT: V 139 LYS cc_start: 0.8491 (tppp) cc_final: 0.8214 (tptp) REVERT: V 239 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8291 (mm-30) REVERT: W 61 ARG cc_start: 0.8057 (mmt180) cc_final: 0.7802 (mmm-85) REVERT: W 78 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8355 (t) REVERT: W 82 GLU cc_start: 0.8359 (tp30) cc_final: 0.8078 (tm-30) REVERT: W 120 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8173 (mm110) REVERT: W 213 GLU cc_start: 0.8410 (tt0) cc_final: 0.8203 (mp0) REVERT: W 244 GLU cc_start: 0.8061 (mt-10) cc_final: 0.6977 (tm-30) REVERT: W 246 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7058 (ttm170) REVERT: X 12 MET cc_start: 0.8929 (tmm) cc_final: 0.8643 (tmm) REVERT: X 66 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8866 (mtpp) REVERT: X 118 GLU cc_start: 0.8177 (tt0) cc_final: 0.7719 (mm-30) REVERT: X 158 MET cc_start: 0.8492 (mtp) cc_final: 0.8258 (mtm) REVERT: X 171 MET cc_start: 0.8991 (tpp) cc_final: 0.8607 (tpp) REVERT: Y 1 MET cc_start: 0.7203 (mmm) cc_final: 0.6819 (mmm) REVERT: Y 72 GLN cc_start: 0.8124 (mt0) cc_final: 0.7748 (mt0) REVERT: Y 76 HIS cc_start: 0.7380 (m-70) cc_final: 0.6685 (p-80) REVERT: Y 116 GLU cc_start: 0.7330 (pm20) cc_final: 0.6988 (pp20) REVERT: Y 180 ARG cc_start: 0.8585 (ttm110) cc_final: 0.8150 (ttp-170) REVERT: Y 206 HIS cc_start: 0.7842 (p90) cc_final: 0.7574 (p90) REVERT: Z 123 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: Z 172 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.8024 (mtm110) REVERT: Z 205 GLN cc_start: 0.7973 (pm20) cc_final: 0.7567 (pm20) REVERT: Z 240 THR cc_start: 0.8014 (m) cc_final: 0.7669 (t) REVERT: Z 244 LYS cc_start: 0.8170 (mttt) cc_final: 0.7870 (mmtp) REVERT: Z 249 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7710 (mp0) REVERT: a 170 GLN cc_start: 0.8730 (tt0) cc_final: 0.8470 (tt0) REVERT: a 201 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8068 (ttmm) REVERT: a 326 LYS cc_start: 0.7718 (pttp) cc_final: 0.7327 (ptmt) REVERT: a 331 GLN cc_start: 0.7787 (mt0) cc_final: 0.7470 (mt0) REVERT: a 332 GLU cc_start: 0.8322 (tt0) cc_final: 0.8100 (tt0) REVERT: b 13 LYS cc_start: 0.8288 (mtmt) cc_final: 0.8048 (mtpm) REVERT: b 64 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7978 (tp30) REVERT: b 163 MET cc_start: 0.8739 (tpp) cc_final: 0.8500 (tpp) outliers start: 143 outliers final: 44 residues processed: 1080 average time/residue: 1.8872 time to fit residues: 2473.5584 Evaluate side-chains 895 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 828 time to evaluate : 5.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 304 ARG Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 246 ARG Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 281 LYS Chi-restraints excluded: chain M residue 201 LYS Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain S residue 107 GLU Chi-restraints excluded: chain S residue 165 SER Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 278 GLN Chi-restraints excluded: chain S residue 282 THR Chi-restraints excluded: chain S residue 307 GLU Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 304 ARG Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 149 SER Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 246 ARG Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 187 SER Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 281 LYS Chi-restraints excluded: chain a residue 201 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 311 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 chunk 467 optimal weight: 0.0770 chunk 382 optimal weight: 0.8980 chunk 154 optimal weight: 8.9990 chunk 562 optimal weight: 8.9990 chunk 607 optimal weight: 6.9990 chunk 500 optimal weight: 4.9990 chunk 557 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 451 optimal weight: 0.9980 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 23 GLN D 223 GLN F 206 ASN F 331 GLN ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN I 166 GLN L 291 GLN M 180 ASN M 244 HIS M 280 ASN N 70 GLN P 93 GLN R 23 GLN R 223 GLN T 206 ASN T 331 GLN V 211 GLN V 266 GLN W 166 GLN Z 291 GLN a 180 ASN a 244 HIS a 280 ASN b 66 ASN b 70 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 49860 Z= 0.184 Angle : 0.533 7.271 67458 Z= 0.285 Chirality : 0.042 0.155 7516 Planarity : 0.004 0.042 8744 Dihedral : 6.122 59.804 7036 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.63 % Favored : 98.31 % Rotamer: Outliers : 2.55 % Allowed : 16.47 % Favored : 80.98 % 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: 0.75 (0.10), residues: 6256 helix: 1.56 (0.11), residues: 2312 sheet: 0.33 (0.12), residues: 1542 loop : -0.35 (0.12), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP V 245 HIS 0.004 0.001 HIS U 198 PHE 0.015 0.001 PHE J 100 TYR 0.019 0.001 TYR P 116 ARG 0.005 0.000 ARG Q 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 907 time to evaluate : 5.977 Fit side-chains REVERT: A 140 MET cc_start: 0.8947 (mmm) cc_final: 0.8507 (mmt) REVERT: A 150 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8138 (mmtp) REVERT: A 215 LYS cc_start: 0.8063 (mttt) cc_final: 0.7662 (mmtt) REVERT: B 16 LYS cc_start: 0.8487 (mttt) cc_final: 0.7935 (mmpt) REVERT: B 21 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8127 (mt-10) REVERT: B 90 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8444 (mtmt) REVERT: B 140 ASN cc_start: 0.8386 (m-40) cc_final: 0.8149 (m110) REVERT: B 169 LYS cc_start: 0.7868 (mtmt) cc_final: 0.7558 (mtmm) REVERT: B 183 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7120 (tp30) REVERT: B 202 THR cc_start: 0.7662 (p) cc_final: 0.7361 (p) REVERT: B 205 ASN cc_start: 0.8283 (p0) cc_final: 0.7892 (p0) REVERT: B 214 ASN cc_start: 0.8310 (p0) cc_final: 0.8083 (m110) REVERT: C 189 MET cc_start: 0.7613 (mtp) cc_final: 0.7025 (ttm) REVERT: C 204 LYS cc_start: 0.8319 (tptm) cc_final: 0.7824 (tttm) REVERT: C 266 GLU cc_start: 0.5644 (mt-10) cc_final: 0.5379 (mm-30) REVERT: D 54 GLN cc_start: 0.8086 (pt0) cc_final: 0.7400 (mm-40) REVERT: D 61 LYS cc_start: 0.8282 (mmtp) cc_final: 0.8014 (tppt) REVERT: D 141 LYS cc_start: 0.8007 (ttmt) cc_final: 0.7730 (mmmt) REVERT: D 180 MET cc_start: 0.8030 (mtm) cc_final: 0.7806 (mtm) REVERT: D 210 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8392 (mt0) REVERT: D 224 LYS cc_start: 0.6800 (mttt) cc_final: 0.6572 (ttpt) REVERT: D 232 GLU cc_start: 0.6151 (tt0) cc_final: 0.5886 (tm-30) REVERT: E 233 MET cc_start: 0.6588 (mmt) cc_final: 0.6263 (mmt) REVERT: E 278 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7590 (mt0) REVERT: E 282 THR cc_start: 0.7743 (OUTLIER) cc_final: 0.7364 (p) REVERT: E 289 MET cc_start: 0.7963 (ptm) cc_final: 0.7543 (ptp) REVERT: E 313 GLU cc_start: 0.7742 (mp0) cc_final: 0.7451 (mp0) REVERT: E 342 MET cc_start: 0.4215 (ttm) cc_final: 0.3533 (tmt) REVERT: F 190 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8192 (m110) REVERT: F 205 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7770 (tttm) REVERT: F 304 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7892 (mtm-85) REVERT: F 390 GLU cc_start: 0.3872 (OUTLIER) cc_final: 0.3407 (mm-30) REVERT: G 33 ASN cc_start: 0.8460 (m-40) cc_final: 0.8239 (m-40) REVERT: G 61 LYS cc_start: 0.7688 (mttt) cc_final: 0.7373 (mmtt) REVERT: G 180 ASP cc_start: 0.7829 (t0) cc_final: 0.7418 (t70) REVERT: H 139 LYS cc_start: 0.8512 (tppp) cc_final: 0.8159 (tttt) REVERT: I 82 GLU cc_start: 0.8368 (tp30) cc_final: 0.8090 (tm-30) REVERT: I 120 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8184 (mm110) REVERT: I 244 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7007 (tm-30) REVERT: J 12 MET cc_start: 0.8930 (tmm) cc_final: 0.8614 (tmm) REVERT: J 66 LYS cc_start: 0.9047 (mtpp) cc_final: 0.8816 (mtpp) REVERT: J 75 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8917 (tmtm) REVERT: J 118 GLU cc_start: 0.8234 (tt0) cc_final: 0.7901 (mm-30) REVERT: J 158 MET cc_start: 0.8441 (mtp) cc_final: 0.7958 (mtt) REVERT: J 171 MET cc_start: 0.8963 (tpp) cc_final: 0.8661 (tpp) REVERT: K 1 MET cc_start: 0.7449 (mmm) cc_final: 0.6958 (mmm) REVERT: K 76 HIS cc_start: 0.7401 (m-70) cc_final: 0.6665 (p-80) REVERT: K 116 GLU cc_start: 0.7527 (pm20) cc_final: 0.7141 (pp20) REVERT: K 206 HIS cc_start: 0.7831 (p90) cc_final: 0.7481 (p90) REVERT: L 205 GLN cc_start: 0.7989 (pm20) cc_final: 0.7626 (pm20) REVERT: L 244 LYS cc_start: 0.8125 (mttt) cc_final: 0.7835 (mmtp) REVERT: L 249 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7849 (mp0) REVERT: M 201 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7946 (mtpt) REVERT: M 326 LYS cc_start: 0.7705 (pttp) cc_final: 0.7323 (ptmt) REVERT: M 331 GLN cc_start: 0.7868 (tt0) cc_final: 0.7507 (mt0) REVERT: M 332 GLU cc_start: 0.8368 (tt0) cc_final: 0.8141 (tt0) REVERT: N 13 LYS cc_start: 0.8342 (mtmt) cc_final: 0.8099 (mtpm) REVERT: N 64 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7909 (tp30) REVERT: O 56 ARG cc_start: 0.7600 (tmm160) cc_final: 0.7337 (tmm160) REVERT: O 140 MET cc_start: 0.8946 (mmm) cc_final: 0.8510 (mmt) REVERT: O 150 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8143 (mmtp) REVERT: O 215 LYS cc_start: 0.7970 (mttt) cc_final: 0.7400 (ttpt) REVERT: P 16 LYS cc_start: 0.8481 (mttt) cc_final: 0.7939 (mmpt) REVERT: P 21 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8116 (mt-10) REVERT: P 90 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8443 (mtmt) REVERT: P 140 ASN cc_start: 0.8373 (m-40) cc_final: 0.8132 (m110) REVERT: P 173 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7638 (tp30) REVERT: P 175 ARG cc_start: 0.7696 (mmm160) cc_final: 0.7137 (mmt180) REVERT: P 183 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7153 (tp30) REVERT: P 202 THR cc_start: 0.7655 (p) cc_final: 0.7327 (p) REVERT: P 204 GLU cc_start: 0.7922 (mp0) cc_final: 0.7517 (mp0) REVERT: P 205 ASN cc_start: 0.8253 (p0) cc_final: 0.7859 (p0) REVERT: P 214 ASN cc_start: 0.8310 (p0) cc_final: 0.8088 (m110) REVERT: Q 61 MET cc_start: 0.8499 (mmm) cc_final: 0.8187 (mmm) REVERT: Q 189 MET cc_start: 0.7634 (mtp) cc_final: 0.7019 (ttm) REVERT: Q 204 LYS cc_start: 0.8315 (tptm) cc_final: 0.7822 (tttm) REVERT: Q 266 GLU cc_start: 0.5748 (mt-10) cc_final: 0.5508 (mm-30) REVERT: R 27 LYS cc_start: 0.8638 (mttp) cc_final: 0.8322 (mmmt) REVERT: R 54 GLN cc_start: 0.8084 (pt0) cc_final: 0.7396 (mm-40) REVERT: R 61 LYS cc_start: 0.8276 (mmtp) cc_final: 0.8005 (tppt) REVERT: R 180 MET cc_start: 0.8085 (mtm) cc_final: 0.7845 (mtm) REVERT: R 210 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8432 (mt0) REVERT: R 224 LYS cc_start: 0.6799 (mttt) cc_final: 0.6572 (ttpt) REVERT: R 232 GLU cc_start: 0.6275 (tt0) cc_final: 0.6032 (tm-30) REVERT: S 144 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7454 (tt0) REVERT: S 233 MET cc_start: 0.6641 (mmt) cc_final: 0.6315 (mmt) REVERT: S 248 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7060 (tt0) REVERT: S 278 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7596 (mt0) REVERT: S 282 THR cc_start: 0.7736 (OUTLIER) cc_final: 0.7352 (p) REVERT: S 289 MET cc_start: 0.7897 (ptm) cc_final: 0.7454 (ptp) REVERT: S 313 GLU cc_start: 0.7860 (mp0) cc_final: 0.7532 (mp0) REVERT: S 342 MET cc_start: 0.4207 (ttm) cc_final: 0.3519 (tmt) REVERT: T 190 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.8196 (m110) REVERT: T 205 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7765 (tttm) REVERT: T 304 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7924 (mtm-85) REVERT: U 33 ASN cc_start: 0.8381 (m-40) cc_final: 0.8085 (m-40) REVERT: U 61 LYS cc_start: 0.7693 (mttt) cc_final: 0.7380 (mmtt) REVERT: U 180 ASP cc_start: 0.7645 (t0) cc_final: 0.7225 (t70) REVERT: V 137 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8792 (m-80) REVERT: V 139 LYS cc_start: 0.8513 (tppp) cc_final: 0.8162 (tttt) REVERT: W 82 GLU cc_start: 0.8361 (tp30) cc_final: 0.8087 (tm-30) REVERT: W 120 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8186 (mm110) REVERT: W 244 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7009 (tm-30) REVERT: X 12 MET cc_start: 0.8934 (tmm) cc_final: 0.8617 (tmm) REVERT: X 66 LYS cc_start: 0.9041 (mtpp) cc_final: 0.8762 (mtpp) REVERT: X 75 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8921 (tmtm) REVERT: X 118 GLU cc_start: 0.8226 (tt0) cc_final: 0.7903 (mm-30) REVERT: X 158 MET cc_start: 0.8456 (mtp) cc_final: 0.7979 (mtt) REVERT: X 171 MET cc_start: 0.8965 (tpp) cc_final: 0.8665 (tpp) REVERT: Y 1 MET cc_start: 0.7428 (mmm) cc_final: 0.7008 (mmm) REVERT: Y 76 HIS cc_start: 0.7391 (m-70) cc_final: 0.6668 (p-80) REVERT: Y 116 GLU cc_start: 0.7565 (pm20) cc_final: 0.7174 (pp20) REVERT: Y 180 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8245 (ttp-110) REVERT: Y 206 HIS cc_start: 0.7821 (p90) cc_final: 0.7483 (p90) REVERT: Z 205 GLN cc_start: 0.7990 (pm20) cc_final: 0.7620 (pm20) REVERT: Z 244 LYS cc_start: 0.8149 (mttt) cc_final: 0.7857 (mmtp) REVERT: Z 249 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7830 (mp0) REVERT: a 201 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7955 (mtpt) REVERT: a 326 LYS cc_start: 0.7707 (pttp) cc_final: 0.7326 (ptmt) REVERT: a 331 GLN cc_start: 0.7663 (mt0) cc_final: 0.7402 (mt0) REVERT: b 1 MET cc_start: 0.7551 (mmm) cc_final: 0.7105 (ptp) REVERT: b 13 LYS cc_start: 0.8287 (mtmt) cc_final: 0.8059 (mtpm) REVERT: b 64 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7909 (tp30) outliers start: 133 outliers final: 51 residues processed: 982 average time/residue: 1.8943 time to fit residues: 2267.6170 Evaluate side-chains 880 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 810 time to evaluate : 5.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 304 ARG Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 281 LYS Chi-restraints excluded: chain M residue 201 LYS Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 119 ILE Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain S residue 107 GLU Chi-restraints excluded: chain S residue 165 SER Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 278 GLN Chi-restraints excluded: chain S residue 282 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 304 ARG Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 116 THR Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 281 LYS Chi-restraints excluded: chain a residue 201 LYS Chi-restraints excluded: chain a residue 257 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 555 optimal weight: 1.9990 chunk 422 optimal weight: 0.9990 chunk 291 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 268 optimal weight: 8.9990 chunk 377 optimal weight: 5.9990 chunk 564 optimal weight: 0.7980 chunk 597 optimal weight: 0.6980 chunk 294 optimal weight: 0.9980 chunk 534 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN C 65 ASN D 23 GLN E 278 GLN E 328 HIS H 211 GLN H 266 GLN K 72 GLN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 291 GLN M 280 ASN N 66 ASN N 70 GLN O 228 ASN R 23 GLN S 278 GLN V 266 GLN Y 72 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN a 180 ASN a 280 ASN b 70 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 49860 Z= 0.166 Angle : 0.499 8.796 67458 Z= 0.266 Chirality : 0.042 0.201 7516 Planarity : 0.004 0.041 8744 Dihedral : 5.445 59.857 7002 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.55 % Favored : 98.42 % Rotamer: Outliers : 2.09 % Allowed : 16.95 % Favored : 80.96 % 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: 6256 helix: 1.89 (0.11), residues: 2318 sheet: 0.40 (0.12), residues: 1550 loop : -0.13 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 165 HIS 0.003 0.001 HIS U 68 PHE 0.012 0.001 PHE X 100 TYR 0.015 0.001 TYR P 116 ARG 0.004 0.000 ARG S 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 864 time to evaluate : 5.676 Fit side-chains REVERT: A 140 MET cc_start: 0.8905 (mmm) cc_final: 0.8615 (mmt) REVERT: A 150 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8082 (mmtt) REVERT: A 215 LYS cc_start: 0.8024 (mttt) cc_final: 0.7490 (ttpt) REVERT: B 16 LYS cc_start: 0.8506 (mttt) cc_final: 0.7986 (mmpt) REVERT: B 90 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8434 (mtmt) REVERT: B 140 ASN cc_start: 0.8365 (m-40) cc_final: 0.8077 (m110) REVERT: B 169 LYS cc_start: 0.7910 (mtmt) cc_final: 0.7707 (mtpp) REVERT: B 173 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7599 (tp30) REVERT: B 183 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7168 (tp30) REVERT: B 195 GLU cc_start: 0.7296 (tp30) cc_final: 0.7038 (tp30) REVERT: B 202 THR cc_start: 0.7663 (p) cc_final: 0.7376 (p) REVERT: B 204 GLU cc_start: 0.7906 (mp0) cc_final: 0.7517 (mp0) REVERT: B 205 ASN cc_start: 0.8176 (p0) cc_final: 0.7836 (p0) REVERT: B 214 ASN cc_start: 0.8283 (p0) cc_final: 0.8053 (m110) REVERT: C 61 MET cc_start: 0.8509 (mmm) cc_final: 0.8246 (mmm) REVERT: C 182 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7502 (mttp) REVERT: C 187 GLU cc_start: 0.7719 (tt0) cc_final: 0.7463 (mp0) REVERT: C 204 LYS cc_start: 0.8185 (tptm) cc_final: 0.7817 (ttmt) REVERT: C 259 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6545 (mm-30) REVERT: C 266 GLU cc_start: 0.5631 (mt-10) cc_final: 0.5353 (mm-30) REVERT: D 54 GLN cc_start: 0.8028 (pt0) cc_final: 0.7337 (mm-40) REVERT: D 61 LYS cc_start: 0.8282 (mmtp) cc_final: 0.8008 (tppt) REVERT: D 141 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7790 (mmmt) REVERT: D 192 SER cc_start: 0.8444 (m) cc_final: 0.8209 (p) REVERT: D 210 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8137 (mt0) REVERT: D 213 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7370 (pt0) REVERT: D 232 GLU cc_start: 0.6283 (tt0) cc_final: 0.5987 (tm-30) REVERT: E 233 MET cc_start: 0.6525 (mmt) cc_final: 0.6215 (mmt) REVERT: E 282 THR cc_start: 0.7859 (m) cc_final: 0.7427 (p) REVERT: E 289 MET cc_start: 0.7884 (ptm) cc_final: 0.7502 (ptp) REVERT: E 313 GLU cc_start: 0.7732 (mp0) cc_final: 0.7442 (mp0) REVERT: E 336 LYS cc_start: 0.6867 (tttp) cc_final: 0.6248 (ttpp) REVERT: E 342 MET cc_start: 0.4180 (ttm) cc_final: 0.3763 (tmt) REVERT: F 205 LYS cc_start: 0.8072 (ttmm) cc_final: 0.7827 (tttm) REVERT: F 304 ARG cc_start: 0.8513 (ttt-90) cc_final: 0.7882 (mtm-85) REVERT: G 33 ASN cc_start: 0.8418 (m-40) cc_final: 0.8168 (m-40) REVERT: G 61 LYS cc_start: 0.7699 (mttt) cc_final: 0.7389 (mmtt) REVERT: H 137 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8721 (m-80) REVERT: H 139 LYS cc_start: 0.8487 (tppp) cc_final: 0.8194 (tttt) REVERT: I 82 GLU cc_start: 0.8364 (tp30) cc_final: 0.8111 (tm-30) REVERT: I 120 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8184 (mm110) REVERT: I 244 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7049 (tm-30) REVERT: J 12 MET cc_start: 0.8923 (tmm) cc_final: 0.8581 (tmm) REVERT: J 66 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8826 (mtpp) REVERT: J 75 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8969 (tmtm) REVERT: J 106 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8031 (mt-10) REVERT: J 118 GLU cc_start: 0.8338 (tt0) cc_final: 0.8050 (tp30) REVERT: J 158 MET cc_start: 0.8422 (mtp) cc_final: 0.7980 (mtt) REVERT: J 171 MET cc_start: 0.8951 (tpp) cc_final: 0.8681 (tpp) REVERT: K 1 MET cc_start: 0.7320 (mmm) cc_final: 0.6872 (mmm) REVERT: K 76 HIS cc_start: 0.7352 (m-70) cc_final: 0.6700 (p-80) REVERT: K 116 GLU cc_start: 0.7638 (pm20) cc_final: 0.7235 (pp20) REVERT: K 180 ARG cc_start: 0.8429 (ttm110) cc_final: 0.8108 (ttp-110) REVERT: L 123 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6880 (tt0) REVERT: L 205 GLN cc_start: 0.7964 (pm20) cc_final: 0.7477 (pm20) REVERT: L 244 LYS cc_start: 0.8096 (mttt) cc_final: 0.7799 (mmtp) REVERT: L 249 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7830 (mp0) REVERT: M 154 ASN cc_start: 0.8848 (m-40) cc_final: 0.8596 (m-40) REVERT: M 201 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7909 (mtpt) REVERT: M 326 LYS cc_start: 0.7712 (pttp) cc_final: 0.7326 (ptmt) REVERT: M 331 GLN cc_start: 0.7867 (tt0) cc_final: 0.7571 (mt0) REVERT: N 13 LYS cc_start: 0.8336 (mtmt) cc_final: 0.8084 (mtpm) REVERT: N 64 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7937 (tp30) REVERT: O 56 ARG cc_start: 0.7657 (tmm160) cc_final: 0.7434 (tmm160) REVERT: O 140 MET cc_start: 0.8907 (mmm) cc_final: 0.8621 (mmt) REVERT: O 150 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8093 (mmtt) REVERT: O 215 LYS cc_start: 0.7991 (mttt) cc_final: 0.7588 (mptt) REVERT: P 16 LYS cc_start: 0.8500 (mttt) cc_final: 0.7902 (mmpt) REVERT: P 90 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8427 (mtmt) REVERT: P 140 ASN cc_start: 0.8357 (m-40) cc_final: 0.8063 (m110) REVERT: P 173 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7567 (tp30) REVERT: P 175 ARG cc_start: 0.7661 (mmm160) cc_final: 0.7090 (mmt180) REVERT: P 183 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7200 (tp30) REVERT: P 195 GLU cc_start: 0.7344 (tp30) cc_final: 0.7075 (tp30) REVERT: P 202 THR cc_start: 0.7631 (p) cc_final: 0.7354 (p) REVERT: P 204 GLU cc_start: 0.7894 (mp0) cc_final: 0.7499 (mp0) REVERT: P 205 ASN cc_start: 0.8164 (p0) cc_final: 0.7817 (p0) REVERT: P 214 ASN cc_start: 0.8282 (p0) cc_final: 0.8053 (m110) REVERT: P 228 LEU cc_start: 0.8232 (mt) cc_final: 0.7880 (mt) REVERT: Q 61 MET cc_start: 0.8475 (mmm) cc_final: 0.8166 (mmm) REVERT: Q 187 GLU cc_start: 0.7721 (tt0) cc_final: 0.7435 (mp0) REVERT: Q 204 LYS cc_start: 0.8186 (tptm) cc_final: 0.7820 (ttmt) REVERT: Q 266 GLU cc_start: 0.5662 (mt-10) cc_final: 0.5405 (mm-30) REVERT: R 54 GLN cc_start: 0.8026 (pt0) cc_final: 0.7334 (mm-40) REVERT: R 141 LYS cc_start: 0.8368 (mtpp) cc_final: 0.7900 (mmtt) REVERT: R 180 MET cc_start: 0.8054 (mtm) cc_final: 0.7851 (mtm) REVERT: R 192 SER cc_start: 0.8439 (m) cc_final: 0.8209 (p) REVERT: R 210 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8211 (mt0) REVERT: R 213 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7378 (pt0) REVERT: R 232 GLU cc_start: 0.6410 (tt0) cc_final: 0.6130 (tm-30) REVERT: S 144 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7480 (tt0) REVERT: S 233 MET cc_start: 0.6519 (mmt) cc_final: 0.6208 (mmt) REVERT: S 282 THR cc_start: 0.7769 (m) cc_final: 0.7316 (p) REVERT: S 313 GLU cc_start: 0.7808 (mp0) cc_final: 0.7490 (mp0) REVERT: S 336 LYS cc_start: 0.6864 (tttp) cc_final: 0.6253 (ttpp) REVERT: S 342 MET cc_start: 0.4123 (ttm) cc_final: 0.3748 (tmt) REVERT: T 205 LYS cc_start: 0.8070 (ttmm) cc_final: 0.7823 (tttm) REVERT: T 304 ARG cc_start: 0.8523 (ttt-90) cc_final: 0.7884 (mtm-85) REVERT: T 390 GLU cc_start: 0.3845 (OUTLIER) cc_final: 0.3395 (mm-30) REVERT: U 33 ASN cc_start: 0.8319 (m-40) cc_final: 0.7987 (m-40) REVERT: U 61 LYS cc_start: 0.7697 (mttt) cc_final: 0.7397 (mmtt) REVERT: V 137 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8794 (m-80) REVERT: V 139 LYS cc_start: 0.8574 (tppp) cc_final: 0.8291 (tttt) REVERT: W 120 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8198 (mm110) REVERT: W 244 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7047 (tm-30) REVERT: X 12 MET cc_start: 0.8930 (tmm) cc_final: 0.8703 (tmm) REVERT: X 66 LYS cc_start: 0.9062 (mtpp) cc_final: 0.8777 (mtpp) REVERT: X 75 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8971 (tmtm) REVERT: X 118 GLU cc_start: 0.8337 (tt0) cc_final: 0.8051 (tp30) REVERT: X 158 MET cc_start: 0.8433 (mtp) cc_final: 0.7986 (mtt) REVERT: X 171 MET cc_start: 0.8953 (tpp) cc_final: 0.8687 (tpp) REVERT: Y 1 MET cc_start: 0.7352 (mmm) cc_final: 0.6859 (mmm) REVERT: Y 76 HIS cc_start: 0.7382 (m-70) cc_final: 0.6746 (p-80) REVERT: Y 116 GLU cc_start: 0.7529 (pm20) cc_final: 0.7124 (pp20) REVERT: Z 205 GLN cc_start: 0.7956 (pm20) cc_final: 0.7569 (pm20) REVERT: Z 244 LYS cc_start: 0.8122 (mttt) cc_final: 0.7823 (mmtp) REVERT: Z 249 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7828 (mp0) REVERT: a 154 ASN cc_start: 0.8871 (m-40) cc_final: 0.8657 (m-40) REVERT: a 201 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7916 (mtpt) REVERT: a 326 LYS cc_start: 0.7776 (pttp) cc_final: 0.7392 (ptmt) REVERT: b 13 LYS cc_start: 0.8288 (mtmt) cc_final: 0.8048 (mtpm) REVERT: b 64 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7940 (tp30) outliers start: 109 outliers final: 55 residues processed: 925 average time/residue: 1.8779 time to fit residues: 2118.2819 Evaluate side-chains 893 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 821 time to evaluate : 5.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 281 LYS Chi-restraints excluded: chain M residue 201 LYS Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain N residue 70 GLN Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain O residue 236 ASN Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 213 GLU Chi-restraints excluded: chain S residue 107 GLU Chi-restraints excluded: chain S residue 165 SER Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 390 GLU Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 116 THR Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 281 LYS Chi-restraints excluded: chain a residue 201 LYS Chi-restraints excluded: chain a residue 257 GLU Chi-restraints excluded: chain b residue 70 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 497 optimal weight: 2.9990 chunk 339 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 444 optimal weight: 0.6980 chunk 246 optimal weight: 0.5980 chunk 509 optimal weight: 2.9990 chunk 412 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 536 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 94 GLN B 223 GLN D 23 GLN E 328 HIS F 190 ASN H 246 ASN H 266 GLN K 72 GLN K 125 GLN L 291 GLN M 280 ASN M 330 GLN N 70 GLN O 228 ASN P 94 GLN R 23 GLN S 328 HIS T 190 ASN V 246 ASN V 266 GLN Y 72 GLN Z 291 GLN a 280 ASN a 330 GLN b 70 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 49860 Z= 0.281 Angle : 0.558 10.330 67458 Z= 0.299 Chirality : 0.044 0.156 7516 Planarity : 0.004 0.044 8744 Dihedral : 5.559 58.582 6980 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.68 % Favored : 98.29 % Rotamer: Outliers : 2.66 % Allowed : 16.89 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.10), residues: 6256 helix: 1.76 (0.11), residues: 2324 sheet: 0.35 (0.12), residues: 1572 loop : -0.11 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 245 HIS 0.005 0.001 HIS U 68 PHE 0.018 0.002 PHE L 260 TYR 0.017 0.002 TYR Y 101 ARG 0.004 0.001 ARG E 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 801 time to evaluate : 7.183 Fit side-chains REVERT: A 140 MET cc_start: 0.8925 (mmm) cc_final: 0.8684 (mmt) REVERT: A 150 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8101 (mmtt) REVERT: A 215 LYS cc_start: 0.7992 (mttt) cc_final: 0.7474 (ttpt) REVERT: B 90 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8535 (mtmt) REVERT: B 140 ASN cc_start: 0.8253 (m-40) cc_final: 0.7948 (m110) REVERT: B 173 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7616 (tp30) REVERT: B 183 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7267 (tp30) REVERT: B 202 THR cc_start: 0.7644 (p) cc_final: 0.7384 (p) REVERT: B 204 GLU cc_start: 0.7919 (mp0) cc_final: 0.7549 (mp0) REVERT: B 205 ASN cc_start: 0.8283 (p0) cc_final: 0.7927 (p0) REVERT: B 214 ASN cc_start: 0.8317 (p0) cc_final: 0.8043 (m110) REVERT: C 204 LYS cc_start: 0.8179 (tptm) cc_final: 0.7799 (ttmt) REVERT: C 259 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6649 (mm-30) REVERT: C 266 GLU cc_start: 0.5658 (mt-10) cc_final: 0.5458 (mm-30) REVERT: D 27 LYS cc_start: 0.8550 (mttp) cc_final: 0.8177 (mmmt) REVERT: D 54 GLN cc_start: 0.8021 (pt0) cc_final: 0.7355 (mm-40) REVERT: D 210 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8255 (mt0) REVERT: D 213 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7353 (pt0) REVERT: D 232 GLU cc_start: 0.6154 (tt0) cc_final: 0.5916 (tm-30) REVERT: E 233 MET cc_start: 0.6642 (mmt) cc_final: 0.6291 (mmt) REVERT: E 257 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: E 282 THR cc_start: 0.7798 (m) cc_final: 0.7371 (p) REVERT: E 313 GLU cc_start: 0.7719 (mp0) cc_final: 0.7459 (mp0) REVERT: E 327 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7986 (tp) REVERT: E 329 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8049 (mmm) REVERT: E 336 LYS cc_start: 0.6890 (tttp) cc_final: 0.6260 (ttpp) REVERT: F 205 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7828 (tttm) REVERT: F 390 GLU cc_start: 0.4042 (OUTLIER) cc_final: 0.3519 (mm-30) REVERT: G 61 LYS cc_start: 0.7691 (mttt) cc_final: 0.7374 (mmtt) REVERT: G 204 GLN cc_start: 0.6132 (OUTLIER) cc_final: 0.5054 (tm130) REVERT: H 139 LYS cc_start: 0.8498 (tppp) cc_final: 0.8185 (tttt) REVERT: I 82 GLU cc_start: 0.8398 (tp30) cc_final: 0.8139 (tm-30) REVERT: I 120 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8094 (mm110) REVERT: J 3 ILE cc_start: 0.8628 (mt) cc_final: 0.8310 (tp) REVERT: J 4 MET cc_start: 0.8878 (tpt) cc_final: 0.8543 (tpp) REVERT: J 12 MET cc_start: 0.8931 (tmm) cc_final: 0.8626 (tmm) REVERT: J 66 LYS cc_start: 0.9076 (mtpp) cc_final: 0.8803 (mtpp) REVERT: J 75 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8962 (tmtm) REVERT: J 106 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7957 (mt-10) REVERT: J 118 GLU cc_start: 0.8345 (tt0) cc_final: 0.8120 (tp30) REVERT: J 158 MET cc_start: 0.8511 (mtp) cc_final: 0.8093 (mtt) REVERT: J 171 MET cc_start: 0.8970 (tpp) cc_final: 0.8699 (tpp) REVERT: J 194 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7996 (ttmm) REVERT: K 1 MET cc_start: 0.7377 (mmm) cc_final: 0.6874 (mmm) REVERT: K 76 HIS cc_start: 0.7392 (m-70) cc_final: 0.6703 (p-80) REVERT: L 123 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6884 (tt0) REVERT: L 205 GLN cc_start: 0.7953 (pm20) cc_final: 0.7459 (pm20) REVERT: L 244 LYS cc_start: 0.8131 (mttt) cc_final: 0.7824 (mmtp) REVERT: L 249 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7795 (mp0) REVERT: M 201 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7996 (mtpt) REVERT: M 326 LYS cc_start: 0.7773 (pttp) cc_final: 0.7381 (ptmt) REVERT: M 331 GLN cc_start: 0.8012 (tt0) cc_final: 0.7651 (mt0) REVERT: N 13 LYS cc_start: 0.8366 (mtmt) cc_final: 0.8103 (mtpm) REVERT: N 64 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7975 (tp30) REVERT: N 70 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: N 195 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8101 (mtp-110) REVERT: O 56 ARG cc_start: 0.7657 (tmm160) cc_final: 0.7387 (mtm110) REVERT: O 140 MET cc_start: 0.8933 (mmm) cc_final: 0.8696 (mmt) REVERT: O 150 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8112 (mmtt) REVERT: O 215 LYS cc_start: 0.7976 (mttt) cc_final: 0.7573 (mmtt) REVERT: P 90 LYS cc_start: 0.8787 (mtpt) cc_final: 0.8532 (mtmt) REVERT: P 140 ASN cc_start: 0.8235 (m-40) cc_final: 0.7931 (m110) REVERT: P 173 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7593 (tp30) REVERT: P 175 ARG cc_start: 0.7863 (mmm160) cc_final: 0.7285 (mmt180) REVERT: P 183 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7284 (tp30) REVERT: P 202 THR cc_start: 0.7637 (p) cc_final: 0.7392 (p) REVERT: P 204 GLU cc_start: 0.7910 (mp0) cc_final: 0.7535 (mp0) REVERT: P 205 ASN cc_start: 0.8270 (p0) cc_final: 0.7925 (p0) REVERT: P 214 ASN cc_start: 0.8325 (p0) cc_final: 0.8048 (m110) REVERT: Q 189 MET cc_start: 0.7429 (mtp) cc_final: 0.7105 (ttm) REVERT: Q 204 LYS cc_start: 0.8183 (tptm) cc_final: 0.7806 (ttmt) REVERT: Q 259 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6614 (mm-30) REVERT: Q 266 GLU cc_start: 0.5674 (mt-10) cc_final: 0.5474 (mm-30) REVERT: R 27 LYS cc_start: 0.8553 (mttp) cc_final: 0.8179 (mmmt) REVERT: R 54 GLN cc_start: 0.8021 (pt0) cc_final: 0.7353 (mm-40) REVERT: R 210 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: R 213 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7356 (pt0) REVERT: R 232 GLU cc_start: 0.6167 (tt0) cc_final: 0.5948 (tm-30) REVERT: S 144 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7610 (tt0) REVERT: S 233 MET cc_start: 0.6633 (mmt) cc_final: 0.6290 (mmt) REVERT: S 257 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: S 282 THR cc_start: 0.7808 (m) cc_final: 0.7382 (p) REVERT: S 313 GLU cc_start: 0.7777 (mp0) cc_final: 0.7510 (mp0) REVERT: S 327 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7986 (tp) REVERT: S 336 LYS cc_start: 0.6887 (tttp) cc_final: 0.6263 (ttpp) REVERT: T 205 LYS cc_start: 0.8107 (ttmm) cc_final: 0.7825 (tttm) REVERT: T 390 GLU cc_start: 0.4055 (OUTLIER) cc_final: 0.3480 (mm-30) REVERT: U 61 LYS cc_start: 0.7717 (mttt) cc_final: 0.7393 (mmtt) REVERT: V 137 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8691 (m-80) REVERT: V 139 LYS cc_start: 0.8556 (tppp) cc_final: 0.8262 (tttt) REVERT: W 120 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8102 (mm110) REVERT: X 12 MET cc_start: 0.8929 (tmm) cc_final: 0.8621 (tmm) REVERT: X 66 LYS cc_start: 0.9099 (mtpp) cc_final: 0.8826 (mtpp) REVERT: X 75 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8960 (tmtm) REVERT: X 118 GLU cc_start: 0.8342 (tt0) cc_final: 0.8123 (tp30) REVERT: X 158 MET cc_start: 0.8525 (mtp) cc_final: 0.7984 (mtt) REVERT: X 171 MET cc_start: 0.8970 (tpp) cc_final: 0.8704 (tpp) REVERT: Y 1 MET cc_start: 0.7365 (mmm) cc_final: 0.6864 (mmm) REVERT: Y 76 HIS cc_start: 0.7395 (m-70) cc_final: 0.6723 (p-80) REVERT: Y 180 ARG cc_start: 0.8416 (ttm110) cc_final: 0.8058 (ttp-110) REVERT: Z 123 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6913 (tt0) REVERT: Z 205 GLN cc_start: 0.7957 (pm20) cc_final: 0.7438 (pm20) REVERT: Z 244 LYS cc_start: 0.8138 (mttt) cc_final: 0.7826 (mmtp) REVERT: Z 249 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7806 (mp0) REVERT: a 201 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7960 (mtpt) REVERT: a 326 LYS cc_start: 0.7769 (pttp) cc_final: 0.7469 (ptmt) REVERT: b 13 LYS cc_start: 0.8344 (mtmt) cc_final: 0.8084 (mtpm) REVERT: b 64 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7968 (tp30) REVERT: b 70 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: b 195 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8111 (mtp-110) outliers start: 139 outliers final: 61 residues processed: 882 average time/residue: 1.9237 time to fit residues: 2065.8456 Evaluate side-chains 857 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 768 time to evaluate : 5.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 280 GLU Chi-restraints excluded: chain M residue 201 LYS Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 70 GLN Chi-restraints excluded: chain N residue 195 ARG Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain O residue 178 MET Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 213 GLU Chi-restraints excluded: chain S residue 165 SER Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 257 ASP Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 307 GLU Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain T residue 227 LYS Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 379 ILE Chi-restraints excluded: chain T residue 390 GLU Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 281 LYS Chi-restraints excluded: chain a residue 201 LYS Chi-restraints excluded: chain a residue 257 GLU Chi-restraints excluded: chain b residue 70 GLN Chi-restraints excluded: chain b residue 195 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 200 optimal weight: 3.9990 chunk 537 optimal weight: 0.3980 chunk 118 optimal weight: 3.9990 chunk 350 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 597 optimal weight: 0.9980 chunk 496 optimal weight: 1.9990 chunk 276 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 313 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN D 23 GLN E 328 HIS F 190 ASN H 266 GLN K 22 ASN K 72 GLN K 125 GLN L 291 GLN M 280 ASN M 303 ASN M 330 GLN N 70 GLN ** O 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 223 GLN R 23 GLN S 328 HIS T 190 ASN V 266 GLN Y 22 ASN Y 72 GLN Z 291 GLN a 280 ASN a 303 ASN a 330 GLN b 70 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 49860 Z= 0.281 Angle : 0.557 8.443 67458 Z= 0.298 Chirality : 0.044 0.151 7516 Planarity : 0.004 0.046 8744 Dihedral : 5.580 59.991 6980 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.73 % Favored : 98.24 % Rotamer: Outliers : 2.76 % Allowed : 17.12 % Favored : 80.12 % 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: 1.00 (0.10), residues: 6256 helix: 1.77 (0.11), residues: 2322 sheet: 0.29 (0.12), residues: 1584 loop : -0.07 (0.13), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP V 245 HIS 0.005 0.001 HIS U 68 PHE 0.017 0.002 PHE Z 260 TYR 0.016 0.002 TYR B 116 ARG 0.004 0.000 ARG Z 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 787 time to evaluate : 6.000 Fit side-chains REVERT: A 56 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7606 (ttm170) REVERT: A 140 MET cc_start: 0.8916 (mmm) cc_final: 0.8687 (mmt) REVERT: A 150 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8073 (mmtt) REVERT: A 215 LYS cc_start: 0.7988 (mttt) cc_final: 0.7598 (mptt) REVERT: B 90 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8527 (mtmt) REVERT: B 140 ASN cc_start: 0.8217 (m-40) cc_final: 0.7888 (m110) REVERT: B 173 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: B 183 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7281 (tp30) REVERT: B 197 PHE cc_start: 0.6187 (t80) cc_final: 0.5877 (t80) REVERT: B 202 THR cc_start: 0.7580 (p) cc_final: 0.7313 (p) REVERT: B 204 GLU cc_start: 0.7919 (mp0) cc_final: 0.7563 (mp0) REVERT: B 205 ASN cc_start: 0.8131 (p0) cc_final: 0.7807 (p0) REVERT: B 214 ASN cc_start: 0.8321 (p0) cc_final: 0.8047 (m110) REVERT: C 204 LYS cc_start: 0.8242 (tptm) cc_final: 0.7866 (ttmt) REVERT: D 27 LYS cc_start: 0.8582 (mttp) cc_final: 0.8214 (mmmt) REVERT: D 54 GLN cc_start: 0.8006 (pt0) cc_final: 0.7346 (mm-40) REVERT: D 210 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8195 (mt0) REVERT: D 213 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7340 (pt0) REVERT: E 233 MET cc_start: 0.6645 (mmt) cc_final: 0.6287 (mmt) REVERT: E 248 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7020 (tt0) REVERT: E 282 THR cc_start: 0.7803 (m) cc_final: 0.7385 (p) REVERT: E 313 GLU cc_start: 0.7621 (mp0) cc_final: 0.7388 (mp0) REVERT: E 327 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.8000 (tp) REVERT: E 329 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8046 (mmm) REVERT: E 336 LYS cc_start: 0.6899 (tttp) cc_final: 0.6257 (ttpp) REVERT: F 205 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7836 (tttm) REVERT: F 390 GLU cc_start: 0.4020 (OUTLIER) cc_final: 0.3395 (mm-30) REVERT: G 61 LYS cc_start: 0.7681 (mttt) cc_final: 0.7341 (mmtt) REVERT: G 204 GLN cc_start: 0.6044 (OUTLIER) cc_final: 0.5141 (tm130) REVERT: H 139 LYS cc_start: 0.8458 (tppp) cc_final: 0.8141 (tttt) REVERT: I 82 GLU cc_start: 0.8396 (tp30) cc_final: 0.8116 (tm-30) REVERT: J 3 ILE cc_start: 0.8640 (mt) cc_final: 0.8315 (tp) REVERT: J 12 MET cc_start: 0.8924 (tmm) cc_final: 0.8594 (tmm) REVERT: J 66 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8824 (mtpp) REVERT: J 75 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8961 (tmtm) REVERT: J 106 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7927 (mt-10) REVERT: J 118 GLU cc_start: 0.8353 (tt0) cc_final: 0.8125 (tp30) REVERT: J 158 MET cc_start: 0.8522 (mtp) cc_final: 0.8279 (mtm) REVERT: K 1 MET cc_start: 0.7464 (mmm) cc_final: 0.6894 (mmm) REVERT: K 76 HIS cc_start: 0.7393 (m-70) cc_final: 0.6720 (p-80) REVERT: K 116 GLU cc_start: 0.7526 (pm20) cc_final: 0.7179 (pp20) REVERT: L 123 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6875 (tt0) REVERT: L 205 GLN cc_start: 0.7975 (pm20) cc_final: 0.7462 (pm20) REVERT: L 244 LYS cc_start: 0.8159 (mttt) cc_final: 0.7847 (mmtp) REVERT: L 249 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7804 (mp0) REVERT: M 326 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7379 (ptmt) REVERT: N 13 LYS cc_start: 0.8355 (mtmt) cc_final: 0.8091 (mtpm) REVERT: N 64 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7976 (tp30) REVERT: N 195 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8104 (mtp-110) REVERT: O 56 ARG cc_start: 0.7669 (tmm160) cc_final: 0.7366 (mtm110) REVERT: O 140 MET cc_start: 0.8920 (mmm) cc_final: 0.8700 (mmt) REVERT: O 150 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8085 (mmtt) REVERT: O 215 LYS cc_start: 0.7956 (mttt) cc_final: 0.7566 (mptt) REVERT: O 248 GLU cc_start: 0.6442 (mt-10) cc_final: 0.5286 (tp30) REVERT: P 90 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8535 (mtmt) REVERT: P 140 ASN cc_start: 0.8214 (m-40) cc_final: 0.7886 (m110) REVERT: P 173 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7563 (tp30) REVERT: P 175 ARG cc_start: 0.7852 (mmm160) cc_final: 0.7276 (mmt180) REVERT: P 183 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7316 (tp30) REVERT: P 204 GLU cc_start: 0.7894 (mp0) cc_final: 0.7488 (mp0) REVERT: P 205 ASN cc_start: 0.8190 (p0) cc_final: 0.7622 (p0) REVERT: P 214 ASN cc_start: 0.8316 (p0) cc_final: 0.8044 (m110) REVERT: Q 204 LYS cc_start: 0.8246 (tptm) cc_final: 0.7938 (tptt) REVERT: Q 210 LYS cc_start: 0.6295 (OUTLIER) cc_final: 0.5771 (mppt) REVERT: R 27 LYS cc_start: 0.8586 (mttp) cc_final: 0.8219 (mmmt) REVERT: R 54 GLN cc_start: 0.8003 (pt0) cc_final: 0.7340 (mm-40) REVERT: R 210 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: R 213 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7314 (pt0) REVERT: S 144 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7598 (tt0) REVERT: S 233 MET cc_start: 0.6638 (mmt) cc_final: 0.6291 (mmt) REVERT: S 282 THR cc_start: 0.7806 (m) cc_final: 0.7379 (p) REVERT: S 313 GLU cc_start: 0.7724 (mp0) cc_final: 0.7460 (mp0) REVERT: S 327 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7986 (tp) REVERT: S 329 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8045 (mmm) REVERT: S 336 LYS cc_start: 0.6885 (tttp) cc_final: 0.6256 (ttpp) REVERT: T 205 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7849 (tttm) REVERT: T 390 GLU cc_start: 0.4008 (OUTLIER) cc_final: 0.3384 (mm-30) REVERT: U 61 LYS cc_start: 0.7687 (mttt) cc_final: 0.7353 (mmtt) REVERT: U 204 GLN cc_start: 0.6332 (OUTLIER) cc_final: 0.5357 (tm130) REVERT: V 137 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8668 (m-80) REVERT: V 139 LYS cc_start: 0.8545 (tppp) cc_final: 0.8248 (tttt) REVERT: X 12 MET cc_start: 0.8924 (tmm) cc_final: 0.8594 (tmm) REVERT: X 66 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8816 (mtpp) REVERT: X 75 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8957 (tmtm) REVERT: X 118 GLU cc_start: 0.8355 (tt0) cc_final: 0.8131 (tp30) REVERT: X 158 MET cc_start: 0.8547 (mtp) cc_final: 0.8304 (mtm) REVERT: X 194 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8024 (ttmm) REVERT: Y 1 MET cc_start: 0.7437 (mmm) cc_final: 0.6869 (mmm) REVERT: Y 76 HIS cc_start: 0.7443 (m-70) cc_final: 0.6762 (p-80) REVERT: Z 123 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6889 (tt0) REVERT: Z 205 GLN cc_start: 0.7977 (pm20) cc_final: 0.7459 (pm20) REVERT: Z 244 LYS cc_start: 0.8166 (mttt) cc_final: 0.7849 (mmtp) REVERT: Z 249 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7822 (mp0) REVERT: a 326 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7396 (ptmt) REVERT: b 13 LYS cc_start: 0.8329 (mtmt) cc_final: 0.8076 (mtpm) REVERT: b 64 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7965 (tp30) REVERT: b 195 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8112 (mtp-110) outliers start: 144 outliers final: 68 residues processed: 872 average time/residue: 1.9646 time to fit residues: 2073.0398 Evaluate side-chains 853 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 758 time to evaluate : 6.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 326 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 195 ARG Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain O residue 178 MET Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 210 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 213 GLU Chi-restraints excluded: chain S residue 165 SER Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 329 MET Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 379 ILE Chi-restraints excluded: chain T residue 390 GLU Chi-restraints excluded: chain U residue 204 GLN Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 194 LYS Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 168 LEU Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain Z residue 130 VAL Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 281 LYS Chi-restraints excluded: chain a residue 257 GLU Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 195 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 576 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 340 optimal weight: 5.9990 chunk 436 optimal weight: 5.9990 chunk 338 optimal weight: 7.9990 chunk 503 optimal weight: 10.0000 chunk 333 optimal weight: 0.7980 chunk 595 optimal weight: 7.9990 chunk 372 optimal weight: 3.9990 chunk 363 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN B 94 GLN D 23 GLN E 314 ASN E 328 HIS F 190 ASN H 266 GLN I 247 GLN K 72 GLN L 291 GLN M 180 ASN M 280 ASN M 303 ASN M 330 GLN N 70 GLN N 94 GLN N 205 HIS P 94 GLN Q 186 HIS R 23 GLN S 314 ASN S 328 HIS T 190 ASN V 266 GLN Y 72 GLN Z 291 GLN a 280 ASN a 303 ASN a 330 GLN b 70 GLN b 94 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 49860 Z= 0.411 Angle : 0.634 9.579 67458 Z= 0.339 Chirality : 0.047 0.157 7516 Planarity : 0.005 0.047 8744 Dihedral : 5.874 56.926 6972 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.92 % Favored : 98.05 % Rotamer: Outliers : 3.05 % Allowed : 16.99 % Favored : 79.97 % 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: 0.79 (0.10), residues: 6256 helix: 1.51 (0.11), residues: 2330 sheet: 0.23 (0.12), residues: 1566 loop : -0.16 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP V 245 HIS 0.007 0.001 HIS U 68 PHE 0.022 0.002 PHE L 260 TYR 0.019 0.002 TYR Y 101 ARG 0.006 0.001 ARG b 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 757 time to evaluate : 5.840 Fit side-chains REVERT: A 56 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7446 (mtm110) REVERT: A 150 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8202 (mmtt) REVERT: A 215 LYS cc_start: 0.7918 (mttt) cc_final: 0.7525 (mptt) REVERT: A 248 GLU cc_start: 0.6498 (mt-10) cc_final: 0.5349 (tp30) REVERT: B 90 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8547 (mtmt) REVERT: B 173 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7764 (tp30) REVERT: B 183 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7128 (tp30) REVERT: B 204 GLU cc_start: 0.7932 (mp0) cc_final: 0.7612 (mp0) REVERT: B 205 ASN cc_start: 0.8012 (p0) cc_final: 0.7689 (p0) REVERT: B 214 ASN cc_start: 0.8348 (p0) cc_final: 0.8068 (m110) REVERT: C 4 ARG cc_start: 0.8458 (mtp-110) cc_final: 0.7980 (mtm110) REVERT: C 204 LYS cc_start: 0.8311 (tptm) cc_final: 0.8002 (tptt) REVERT: D 27 LYS cc_start: 0.8593 (mttp) cc_final: 0.8238 (mmmt) REVERT: D 54 GLN cc_start: 0.8006 (pt0) cc_final: 0.7362 (mm-40) REVERT: D 210 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8207 (mt0) REVERT: D 213 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: E 233 MET cc_start: 0.6650 (mmt) cc_final: 0.6301 (mmt) REVERT: E 248 GLU cc_start: 0.7306 (mm-30) cc_final: 0.7008 (tt0) REVERT: E 282 THR cc_start: 0.7946 (m) cc_final: 0.7524 (p) REVERT: E 313 GLU cc_start: 0.7637 (mp0) cc_final: 0.7412 (mp0) REVERT: E 327 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8005 (tp) REVERT: E 329 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8058 (mmm) REVERT: F 205 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7927 (tttm) REVERT: F 221 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6286 (mt) REVERT: F 276 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8449 (ptt) REVERT: F 390 GLU cc_start: 0.4154 (OUTLIER) cc_final: 0.3496 (mm-30) REVERT: G 61 LYS cc_start: 0.7741 (mttt) cc_final: 0.7381 (mmtt) REVERT: G 204 GLN cc_start: 0.6319 (OUTLIER) cc_final: 0.5357 (tm130) REVERT: H 139 LYS cc_start: 0.8600 (tppp) cc_final: 0.8225 (ttpt) REVERT: I 120 GLN cc_start: 0.8372 (mm110) cc_final: 0.8068 (mm110) REVERT: I 209 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7385 (tppt) REVERT: I 213 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: J 3 ILE cc_start: 0.8626 (mt) cc_final: 0.8260 (tp) REVERT: J 12 MET cc_start: 0.8908 (tmm) cc_final: 0.8630 (tmm) REVERT: J 66 LYS cc_start: 0.9076 (mtpp) cc_final: 0.8852 (mtpp) REVERT: J 75 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8961 (tmtm) REVERT: J 106 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8008 (mt-10) REVERT: J 118 GLU cc_start: 0.8394 (tt0) cc_final: 0.8099 (tp30) REVERT: J 158 MET cc_start: 0.8621 (mtp) cc_final: 0.8098 (mtm) REVERT: J 194 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8036 (ttmm) REVERT: K 1 MET cc_start: 0.7238 (mmm) cc_final: 0.6436 (mmm) REVERT: K 3 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: K 76 HIS cc_start: 0.7348 (m-70) cc_final: 0.6667 (p-80) REVERT: K 80 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8483 (mp0) REVERT: L 123 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6902 (tt0) REVERT: L 205 GLN cc_start: 0.7986 (pm20) cc_final: 0.7563 (pm20) REVERT: L 244 LYS cc_start: 0.8211 (mttt) cc_final: 0.7919 (mmtp) REVERT: L 249 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7812 (mp0) REVERT: M 326 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7465 (ptmt) REVERT: N 13 LYS cc_start: 0.8396 (mtmt) cc_final: 0.8137 (mtpm) REVERT: N 64 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7986 (tp30) REVERT: N 195 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8109 (mtp-110) REVERT: O 56 ARG cc_start: 0.7660 (tmm160) cc_final: 0.7359 (mtm110) REVERT: O 150 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8208 (mmtt) REVERT: O 215 LYS cc_start: 0.7900 (mttt) cc_final: 0.7502 (mptt) REVERT: O 248 GLU cc_start: 0.6482 (mt-10) cc_final: 0.5332 (tp30) REVERT: P 90 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8544 (mtmt) REVERT: P 173 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7781 (tp30) REVERT: P 175 ARG cc_start: 0.7908 (mmm160) cc_final: 0.7270 (mmt180) REVERT: P 183 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7171 (tp30) REVERT: P 204 GLU cc_start: 0.8077 (mp0) cc_final: 0.7651 (mp0) REVERT: P 205 ASN cc_start: 0.8060 (p0) cc_final: 0.7389 (p0) REVERT: P 214 ASN cc_start: 0.8342 (p0) cc_final: 0.8064 (m110) REVERT: Q 4 ARG cc_start: 0.8462 (mtp-110) cc_final: 0.7985 (mtm110) REVERT: Q 204 LYS cc_start: 0.8305 (tptm) cc_final: 0.7927 (ttmt) REVERT: Q 210 LYS cc_start: 0.6353 (OUTLIER) cc_final: 0.5828 (mppt) REVERT: R 27 LYS cc_start: 0.8593 (mttp) cc_final: 0.8238 (mmmt) REVERT: R 54 GLN cc_start: 0.8004 (pt0) cc_final: 0.7358 (mm-40) REVERT: R 210 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8303 (mt0) REVERT: R 213 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7452 (pt0) REVERT: S 233 MET cc_start: 0.6647 (mmt) cc_final: 0.6287 (mmt) REVERT: S 282 THR cc_start: 0.7852 (m) cc_final: 0.7422 (p) REVERT: S 313 GLU cc_start: 0.7731 (mp0) cc_final: 0.7487 (mp0) REVERT: S 327 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8005 (tp) REVERT: S 329 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8049 (mmm) REVERT: T 205 LYS cc_start: 0.8221 (ttmm) cc_final: 0.7918 (tttm) REVERT: T 221 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6308 (mt) REVERT: T 276 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8420 (ptt) REVERT: T 390 GLU cc_start: 0.3843 (OUTLIER) cc_final: 0.3318 (mm-30) REVERT: U 61 LYS cc_start: 0.7739 (mttt) cc_final: 0.7391 (mmtt) REVERT: U 204 GLN cc_start: 0.6367 (OUTLIER) cc_final: 0.5390 (tm130) REVERT: V 137 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: V 139 LYS cc_start: 0.8601 (tppp) cc_final: 0.8230 (ttpt) REVERT: W 120 GLN cc_start: 0.8378 (mm110) cc_final: 0.8074 (mm110) REVERT: W 209 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7380 (tppt) REVERT: W 213 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: X 12 MET cc_start: 0.8904 (tmm) cc_final: 0.8622 (tmm) REVERT: X 75 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8961 (tmtm) REVERT: X 118 GLU cc_start: 0.8392 (tt0) cc_final: 0.8100 (tp30) REVERT: X 194 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8030 (ttmm) REVERT: Y 1 MET cc_start: 0.7399 (mmm) cc_final: 0.6837 (mmm) REVERT: Y 76 HIS cc_start: 0.7370 (m-70) cc_final: 0.6708 (p-80) REVERT: Y 80 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8476 (mp0) REVERT: Z 123 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6885 (tt0) REVERT: Z 205 GLN cc_start: 0.7986 (pm20) cc_final: 0.7557 (pm20) REVERT: Z 244 LYS cc_start: 0.8213 (mttt) cc_final: 0.7917 (mmtp) REVERT: Z 249 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7802 (mp0) REVERT: a 157 PHE cc_start: 0.7424 (m-80) cc_final: 0.7221 (m-10) REVERT: a 326 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7423 (ptmt) REVERT: b 13 LYS cc_start: 0.8383 (mtmt) cc_final: 0.8122 (mtpm) REVERT: b 64 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7984 (tp30) REVERT: b 195 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8116 (mtp-110) outliers start: 159 outliers final: 69 residues processed: 850 average time/residue: 1.9546 time to fit residues: 2013.6867 Evaluate side-chains 821 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 715 time to evaluate : 5.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 291 GLN Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 310 GLU Chi-restraints excluded: chain M residue 326 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 195 ARG Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 210 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 213 GLU Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain S residue 314 ASN Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 329 MET Chi-restraints excluded: chain T residue 186 ILE Chi-restraints excluded: chain T residue 221 LEU Chi-restraints excluded: chain T residue 276 MET Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 390 GLU Chi-restraints excluded: chain U residue 204 GLN Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain W residue 209 LYS Chi-restraints excluded: chain W residue 213 GLU Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 194 LYS Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 168 LEU Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain Z residue 130 VAL Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 281 LYS Chi-restraints excluded: chain a residue 257 GLU Chi-restraints excluded: chain a residue 310 GLU Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 195 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 368 optimal weight: 1.9990 chunk 237 optimal weight: 0.0470 chunk 355 optimal weight: 5.9990 chunk 179 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 378 optimal weight: 7.9990 chunk 405 optimal weight: 3.9990 chunk 294 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 468 optimal weight: 4.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 GLN C 30 GLN C 186 HIS D 23 GLN E 328 HIS F 190 ASN H 266 GLN K 72 GLN K 125 GLN M 280 ASN M 303 ASN M 330 GLN N 70 GLN N 205 HIS Q 186 HIS R 23 GLN S 328 HIS T 190 ASN V 266 GLN W 247 GLN Y 72 GLN Z 291 GLN a 280 ASN a 303 ASN a 330 GLN b 70 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 49860 Z= 0.191 Angle : 0.514 7.478 67458 Z= 0.275 Chirality : 0.042 0.150 7516 Planarity : 0.004 0.046 8744 Dihedral : 5.417 59.670 6972 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.66 % Favored : 98.31 % Rotamer: Outliers : 1.99 % Allowed : 18.23 % Favored : 79.77 % 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: 1.05 (0.10), residues: 6256 helix: 1.85 (0.11), residues: 2332 sheet: 0.26 (0.12), residues: 1570 loop : -0.05 (0.13), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 245 HIS 0.003 0.001 HIS U 68 PHE 0.013 0.001 PHE J 100 TYR 0.015 0.001 TYR P 116 ARG 0.003 0.000 ARG R 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 797 time to evaluate : 6.019 Fit side-chains REVERT: A 56 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7502 (mtm110) REVERT: A 215 LYS cc_start: 0.7892 (mttt) cc_final: 0.7537 (mptt) REVERT: A 248 GLU cc_start: 0.6500 (mt-10) cc_final: 0.5346 (tp30) REVERT: B 90 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8474 (mtmt) REVERT: B 183 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7094 (tp30) REVERT: B 197 PHE cc_start: 0.6067 (t80) cc_final: 0.5741 (t80) REVERT: B 204 GLU cc_start: 0.7873 (mp0) cc_final: 0.7524 (mp0) REVERT: B 205 ASN cc_start: 0.7823 (p0) cc_final: 0.7585 (p0) REVERT: B 214 ASN cc_start: 0.8314 (p0) cc_final: 0.8040 (m110) REVERT: C 204 LYS cc_start: 0.8261 (tptm) cc_final: 0.7942 (tptt) REVERT: D 27 LYS cc_start: 0.8528 (mttp) cc_final: 0.8167 (mmmt) REVERT: D 54 GLN cc_start: 0.7978 (pt0) cc_final: 0.7235 (mm-40) REVERT: D 61 LYS cc_start: 0.8362 (mmtp) cc_final: 0.8141 (mtpp) REVERT: D 192 SER cc_start: 0.8593 (m) cc_final: 0.8290 (p) REVERT: D 210 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: D 213 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7469 (pt0) REVERT: E 233 MET cc_start: 0.6729 (mmt) cc_final: 0.6356 (mmt) REVERT: E 282 THR cc_start: 0.7859 (m) cc_final: 0.7431 (p) REVERT: E 313 GLU cc_start: 0.7383 (mp0) cc_final: 0.7136 (mp0) REVERT: E 327 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7948 (tp) REVERT: E 329 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8037 (mmm) REVERT: F 205 LYS cc_start: 0.8067 (ttmm) cc_final: 0.7820 (tmtt) REVERT: F 390 GLU cc_start: 0.4068 (OUTLIER) cc_final: 0.3439 (mm-30) REVERT: G 61 LYS cc_start: 0.7583 (mttt) cc_final: 0.7238 (mmtt) REVERT: H 139 LYS cc_start: 0.8523 (tppp) cc_final: 0.8165 (tttt) REVERT: I 213 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: J 3 ILE cc_start: 0.8615 (mt) cc_final: 0.8293 (tp) REVERT: J 12 MET cc_start: 0.8913 (tmm) cc_final: 0.8650 (tmm) REVERT: J 75 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8954 (tmtm) REVERT: J 106 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7961 (mt-10) REVERT: J 118 GLU cc_start: 0.8373 (tt0) cc_final: 0.8044 (tp30) REVERT: K 1 MET cc_start: 0.7103 (mmm) cc_final: 0.6385 (mmm) REVERT: K 76 HIS cc_start: 0.7359 (m-70) cc_final: 0.6748 (p-80) REVERT: L 123 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6806 (tt0) REVERT: L 138 ASP cc_start: 0.7576 (m-30) cc_final: 0.7338 (m-30) REVERT: L 139 TYR cc_start: 0.7667 (m-80) cc_final: 0.6936 (p90) REVERT: L 205 GLN cc_start: 0.7917 (pm20) cc_final: 0.7451 (pm20) REVERT: L 244 LYS cc_start: 0.8126 (mttt) cc_final: 0.7830 (mmtp) REVERT: L 249 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7815 (mp0) REVERT: M 326 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7194 (ttmt) REVERT: N 13 LYS cc_start: 0.8297 (mtmt) cc_final: 0.8032 (mtpm) REVERT: N 26 TYR cc_start: 0.8602 (t80) cc_final: 0.8295 (t80) REVERT: N 64 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7969 (tp30) REVERT: O 56 ARG cc_start: 0.7639 (tmm160) cc_final: 0.7364 (mtm110) REVERT: O 215 LYS cc_start: 0.7886 (mttt) cc_final: 0.7538 (mptt) REVERT: O 248 GLU cc_start: 0.6481 (mt-10) cc_final: 0.5324 (tp30) REVERT: P 90 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8470 (mtmt) REVERT: P 175 ARG cc_start: 0.7824 (mmm160) cc_final: 0.7243 (mmt180) REVERT: P 183 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7102 (tp30) REVERT: P 204 GLU cc_start: 0.7868 (mp0) cc_final: 0.7468 (mp0) REVERT: P 205 ASN cc_start: 0.8204 (p0) cc_final: 0.7701 (p0) REVERT: P 214 ASN cc_start: 0.8305 (p0) cc_final: 0.8037 (m110) REVERT: Q 204 LYS cc_start: 0.8238 (tptm) cc_final: 0.7908 (tppt) REVERT: Q 210 LYS cc_start: 0.6074 (OUTLIER) cc_final: 0.5584 (mppt) REVERT: R 54 GLN cc_start: 0.8033 (pt0) cc_final: 0.7278 (mm-40) REVERT: R 192 SER cc_start: 0.8581 (m) cc_final: 0.8284 (p) REVERT: R 210 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8213 (mt0) REVERT: R 213 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: S 233 MET cc_start: 0.6720 (mmt) cc_final: 0.6369 (mmt) REVERT: S 282 THR cc_start: 0.7855 (m) cc_final: 0.7429 (p) REVERT: S 313 GLU cc_start: 0.7697 (mp0) cc_final: 0.7473 (mp0) REVERT: S 327 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7952 (tp) REVERT: S 329 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8032 (mmm) REVERT: T 205 LYS cc_start: 0.8081 (ttmm) cc_final: 0.7830 (tmtt) REVERT: T 276 MET cc_start: 0.8611 (ttm) cc_final: 0.8393 (ptt) REVERT: T 390 GLU cc_start: 0.4174 (OUTLIER) cc_final: 0.3505 (mm-30) REVERT: U 33 ASN cc_start: 0.8297 (m-40) cc_final: 0.8050 (m110) REVERT: U 61 LYS cc_start: 0.7583 (mttt) cc_final: 0.7244 (mmtt) REVERT: U 204 GLN cc_start: 0.6438 (OUTLIER) cc_final: 0.5485 (tm130) REVERT: V 137 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8644 (m-80) REVERT: V 139 LYS cc_start: 0.8582 (tppp) cc_final: 0.8270 (tttt) REVERT: W 213 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: X 12 MET cc_start: 0.8919 (tmm) cc_final: 0.8652 (tmm) REVERT: X 75 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8978 (tmtm) REVERT: X 106 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7985 (mt-10) REVERT: X 118 GLU cc_start: 0.8367 (tt0) cc_final: 0.8043 (tp30) REVERT: Y 1 MET cc_start: 0.7354 (mmm) cc_final: 0.6818 (mmm) REVERT: Y 76 HIS cc_start: 0.7374 (m-70) cc_final: 0.6793 (p-80) REVERT: Z 123 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6806 (tt0) REVERT: Z 138 ASP cc_start: 0.7648 (m-30) cc_final: 0.7424 (m-30) REVERT: Z 139 TYR cc_start: 0.7603 (m-80) cc_final: 0.7014 (p90) REVERT: Z 205 GLN cc_start: 0.7914 (pm20) cc_final: 0.7444 (pm20) REVERT: Z 244 LYS cc_start: 0.8134 (mttt) cc_final: 0.7838 (mmtp) REVERT: Z 249 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7816 (mp0) REVERT: a 292 MET cc_start: 0.7722 (ttm) cc_final: 0.7466 (ttp) REVERT: a 326 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7112 (ttmt) REVERT: b 64 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7966 (tp30) outliers start: 104 outliers final: 50 residues processed: 863 average time/residue: 1.8829 time to fit residues: 1975.2211 Evaluate side-chains 834 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 763 time to evaluate : 5.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 326 LYS Chi-restraints excluded: chain N residue 70 GLN Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain Q residue 210 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 213 GLU Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 329 MET Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 390 GLU Chi-restraints excluded: chain U residue 204 GLN Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain W residue 213 GLU Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain Y residue 168 LEU Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain a residue 257 GLU Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 70 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 541 optimal weight: 2.9990 chunk 570 optimal weight: 4.9990 chunk 520 optimal weight: 0.9990 chunk 555 optimal weight: 3.9990 chunk 334 optimal weight: 4.9990 chunk 241 optimal weight: 0.0370 chunk 435 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 501 optimal weight: 3.9990 chunk 524 optimal weight: 0.8980 chunk 553 optimal weight: 0.8980 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 HIS D 23 GLN E 328 HIS F 190 ASN H 266 GLN K 72 GLN K 125 GLN M 280 ASN M 303 ASN M 330 GLN N 70 GLN N 205 HIS Q 186 HIS R 23 GLN S 328 HIS T 190 ASN V 266 GLN Y 72 GLN Z 291 GLN a 180 ASN a 280 ASN a 303 ASN a 330 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 49860 Z= 0.201 Angle : 0.520 8.700 67458 Z= 0.277 Chirality : 0.042 0.146 7516 Planarity : 0.004 0.045 8744 Dihedral : 5.319 59.017 6964 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Rotamer: Outliers : 1.69 % Allowed : 18.58 % Favored : 79.74 % 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: 1.10 (0.10), residues: 6256 helix: 1.91 (0.11), residues: 2328 sheet: 0.26 (0.12), residues: 1574 loop : -0.02 (0.13), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 245 HIS 0.004 0.001 HIS G 68 PHE 0.013 0.001 PHE J 100 TYR 0.015 0.001 TYR P 116 ARG 0.008 0.000 ARG N 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 780 time to evaluate : 6.010 Fit side-chains REVERT: A 56 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7513 (mtm110) REVERT: A 215 LYS cc_start: 0.7891 (mttt) cc_final: 0.7337 (ttpt) REVERT: A 248 GLU cc_start: 0.6502 (mt-10) cc_final: 0.5311 (tp30) REVERT: B 90 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8478 (mtmt) REVERT: B 183 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7262 (tp30) REVERT: B 197 PHE cc_start: 0.6058 (t80) cc_final: 0.5740 (t80) REVERT: B 204 GLU cc_start: 0.7875 (mp0) cc_final: 0.7529 (mp0) REVERT: B 205 ASN cc_start: 0.8150 (p0) cc_final: 0.7862 (p0) REVERT: B 214 ASN cc_start: 0.8293 (p0) cc_final: 0.8020 (m110) REVERT: C 182 LYS cc_start: 0.7741 (ttmt) cc_final: 0.7496 (mttm) REVERT: C 204 LYS cc_start: 0.8209 (tptm) cc_final: 0.7883 (tppt) REVERT: D 27 LYS cc_start: 0.8518 (mttp) cc_final: 0.8176 (mmmt) REVERT: D 54 GLN cc_start: 0.7966 (pt0) cc_final: 0.7346 (mm-40) REVERT: D 61 LYS cc_start: 0.8359 (mmtp) cc_final: 0.8128 (mtpp) REVERT: D 192 SER cc_start: 0.8590 (m) cc_final: 0.8294 (p) REVERT: D 210 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8125 (mt0) REVERT: D 213 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7462 (pt0) REVERT: E 233 MET cc_start: 0.6535 (mmt) cc_final: 0.6235 (mmt) REVERT: E 282 THR cc_start: 0.7856 (m) cc_final: 0.7438 (p) REVERT: E 327 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7974 (tp) REVERT: E 329 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8039 (mmm) REVERT: F 205 LYS cc_start: 0.8105 (ttmm) cc_final: 0.7859 (tmtt) REVERT: F 221 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5985 (mt) REVERT: F 376 THR cc_start: 0.8620 (m) cc_final: 0.8297 (p) REVERT: F 390 GLU cc_start: 0.4109 (OUTLIER) cc_final: 0.3664 (mm-30) REVERT: G 61 LYS cc_start: 0.7597 (mttt) cc_final: 0.7241 (mmtt) REVERT: H 139 LYS cc_start: 0.8515 (tppp) cc_final: 0.8185 (tttt) REVERT: I 120 GLN cc_start: 0.8330 (mm110) cc_final: 0.8107 (mm110) REVERT: I 213 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: J 3 ILE cc_start: 0.8557 (mt) cc_final: 0.8202 (tp) REVERT: J 12 MET cc_start: 0.8929 (tmm) cc_final: 0.8647 (tmm) REVERT: J 75 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8976 (tmtm) REVERT: J 106 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7880 (mt-10) REVERT: J 118 GLU cc_start: 0.8389 (tt0) cc_final: 0.8054 (tp30) REVERT: K 1 MET cc_start: 0.7157 (mmm) cc_final: 0.6444 (mmm) REVERT: K 76 HIS cc_start: 0.7390 (m-70) cc_final: 0.6762 (p-80) REVERT: L 123 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6793 (tt0) REVERT: L 138 ASP cc_start: 0.7688 (m-30) cc_final: 0.7456 (m-30) REVERT: L 139 TYR cc_start: 0.7603 (m-80) cc_final: 0.7082 (p90) REVERT: L 205 GLN cc_start: 0.7932 (pm20) cc_final: 0.7446 (pm20) REVERT: L 244 LYS cc_start: 0.8136 (mttt) cc_final: 0.7775 (mmtp) REVERT: L 249 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7803 (mp0) REVERT: M 326 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7262 (ttmt) REVERT: N 26 TYR cc_start: 0.8625 (t80) cc_final: 0.8290 (t80) REVERT: N 64 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7925 (tp30) REVERT: O 56 ARG cc_start: 0.7653 (tmm160) cc_final: 0.7367 (ttp80) REVERT: O 215 LYS cc_start: 0.7874 (mttt) cc_final: 0.7513 (mptt) REVERT: O 248 GLU cc_start: 0.6482 (mt-10) cc_final: 0.5333 (tp30) REVERT: P 90 LYS cc_start: 0.8730 (mtpt) cc_final: 0.8472 (mtmt) REVERT: P 175 ARG cc_start: 0.7838 (mmm160) cc_final: 0.7248 (mmt180) REVERT: P 183 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7108 (tp30) REVERT: P 204 GLU cc_start: 0.7875 (mp0) cc_final: 0.7519 (mp0) REVERT: P 205 ASN cc_start: 0.8173 (p0) cc_final: 0.7684 (p0) REVERT: P 214 ASN cc_start: 0.8289 (p0) cc_final: 0.8015 (m110) REVERT: Q 204 LYS cc_start: 0.8198 (tptm) cc_final: 0.7875 (tppt) REVERT: Q 210 LYS cc_start: 0.6120 (OUTLIER) cc_final: 0.5627 (mppt) REVERT: R 54 GLN cc_start: 0.7965 (pt0) cc_final: 0.7339 (mm-40) REVERT: R 61 LYS cc_start: 0.8175 (mmmm) cc_final: 0.7894 (tppt) REVERT: R 192 SER cc_start: 0.8596 (m) cc_final: 0.8300 (p) REVERT: R 210 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8158 (mt0) REVERT: R 213 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: S 233 MET cc_start: 0.6651 (mmt) cc_final: 0.6333 (mmt) REVERT: S 282 THR cc_start: 0.7854 (m) cc_final: 0.7436 (p) REVERT: S 313 GLU cc_start: 0.7492 (mp0) cc_final: 0.7273 (mp0) REVERT: S 327 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7974 (tp) REVERT: S 329 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8031 (mmm) REVERT: T 205 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7842 (tmtt) REVERT: T 221 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.6071 (mt) REVERT: T 276 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8383 (ptt) REVERT: T 390 GLU cc_start: 0.4304 (OUTLIER) cc_final: 0.3700 (mm-30) REVERT: U 33 ASN cc_start: 0.8296 (m-40) cc_final: 0.8037 (m110) REVERT: U 61 LYS cc_start: 0.7597 (mttt) cc_final: 0.7253 (mmtt) REVERT: U 204 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.5535 (tm-30) REVERT: V 137 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8692 (m-80) REVERT: V 139 LYS cc_start: 0.8553 (tppp) cc_final: 0.8256 (tttt) REVERT: W 120 GLN cc_start: 0.8336 (mm110) cc_final: 0.8113 (mm110) REVERT: W 213 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: X 12 MET cc_start: 0.8945 (tmm) cc_final: 0.8656 (tmm) REVERT: X 75 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8974 (tmtm) REVERT: X 106 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7965 (mt-10) REVERT: X 118 GLU cc_start: 0.8383 (tt0) cc_final: 0.8054 (tp30) REVERT: Y 1 MET cc_start: 0.7331 (mmm) cc_final: 0.6791 (mmm) REVERT: Y 76 HIS cc_start: 0.7380 (m-70) cc_final: 0.6782 (p-80) REVERT: Z 123 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6805 (tt0) REVERT: Z 138 ASP cc_start: 0.7713 (m-30) cc_final: 0.7448 (m-30) REVERT: Z 139 TYR cc_start: 0.7645 (m-80) cc_final: 0.7077 (p90) REVERT: Z 205 GLN cc_start: 0.7932 (pm20) cc_final: 0.7441 (pm20) REVERT: Z 244 LYS cc_start: 0.8150 (mttt) cc_final: 0.7826 (mmtp) REVERT: Z 249 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7813 (mp0) REVERT: a 326 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7201 (ttmt) REVERT: b 64 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7919 (tp30) outliers start: 88 outliers final: 49 residues processed: 836 average time/residue: 1.9203 time to fit residues: 1976.6558 Evaluate side-chains 839 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 766 time to evaluate : 5.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 326 LYS Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain Q residue 210 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 213 GLU Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 329 MET Chi-restraints excluded: chain T residue 221 LEU Chi-restraints excluded: chain T residue 276 MET Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 390 GLU Chi-restraints excluded: chain U residue 204 GLN Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain W residue 213 GLU Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 168 LEU Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain a residue 257 GLU Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 333 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 364 optimal weight: 7.9990 chunk 586 optimal weight: 3.9990 chunk 358 optimal weight: 7.9990 chunk 278 optimal weight: 0.9980 chunk 408 optimal weight: 0.9990 chunk 615 optimal weight: 6.9990 chunk 566 optimal weight: 5.9990 chunk 490 optimal weight: 0.4980 chunk 50 optimal weight: 10.0000 chunk 378 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 HIS D 23 GLN E 255 GLN E 328 HIS F 190 ASN H 266 GLN K 72 GLN K 125 GLN L 291 GLN M 280 ASN M 303 ASN M 330 GLN N 70 GLN Q 186 HIS R 23 GLN S 255 GLN S 328 HIS T 190 ASN V 266 GLN Y 72 GLN Z 291 GLN a 280 ASN a 303 ASN a 330 GLN b 70 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 49860 Z= 0.248 Angle : 0.545 7.637 67458 Z= 0.290 Chirality : 0.043 0.145 7516 Planarity : 0.004 0.046 8744 Dihedral : 5.435 58.797 6964 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.84 % Favored : 98.13 % Rotamer: Outliers : 1.65 % Allowed : 18.69 % Favored : 79.66 % 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: 1.05 (0.10), residues: 6256 helix: 1.84 (0.11), residues: 2334 sheet: 0.24 (0.12), residues: 1574 loop : -0.03 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP V 245 HIS 0.005 0.001 HIS G 68 PHE 0.016 0.002 PHE T 389 TYR 0.015 0.002 TYR P 116 ARG 0.007 0.000 ARG Z 288 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 754 time to evaluate : 5.755 Fit side-chains REVERT: A 56 ARG cc_start: 0.7904 (ttp80) cc_final: 0.7502 (mtm110) REVERT: A 215 LYS cc_start: 0.7892 (mttt) cc_final: 0.7328 (ttpt) REVERT: A 248 GLU cc_start: 0.6498 (mt-10) cc_final: 0.5347 (tp30) REVERT: B 90 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8511 (mtmt) REVERT: B 140 ASN cc_start: 0.8202 (m-40) cc_final: 0.7996 (m110) REVERT: B 183 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7257 (tp30) REVERT: B 197 PHE cc_start: 0.6174 (t80) cc_final: 0.5840 (t80) REVERT: B 204 GLU cc_start: 0.7909 (mp0) cc_final: 0.7569 (mp0) REVERT: B 205 ASN cc_start: 0.8178 (p0) cc_final: 0.7887 (p0) REVERT: B 214 ASN cc_start: 0.8309 (p0) cc_final: 0.8032 (m110) REVERT: C 204 LYS cc_start: 0.8216 (tptm) cc_final: 0.7907 (tppt) REVERT: D 27 LYS cc_start: 0.8529 (mttp) cc_final: 0.8217 (mmmt) REVERT: D 54 GLN cc_start: 0.7912 (pt0) cc_final: 0.7299 (mm-40) REVERT: D 61 LYS cc_start: 0.8381 (mmtp) cc_final: 0.8143 (mtpp) REVERT: D 210 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: D 213 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: E 233 MET cc_start: 0.6660 (mmt) cc_final: 0.6316 (mmt) REVERT: E 282 THR cc_start: 0.7950 (m) cc_final: 0.7547 (p) REVERT: E 327 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7993 (tp) REVERT: E 329 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8041 (mmm) REVERT: F 205 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7908 (tmtt) REVERT: F 221 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.6060 (mt) REVERT: F 390 GLU cc_start: 0.4221 (OUTLIER) cc_final: 0.3782 (mm-30) REVERT: G 61 LYS cc_start: 0.7671 (mttt) cc_final: 0.7324 (mmtt) REVERT: H 139 LYS cc_start: 0.8514 (tppp) cc_final: 0.8180 (tttt) REVERT: I 213 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: J 3 ILE cc_start: 0.8603 (mt) cc_final: 0.8253 (tp) REVERT: J 12 MET cc_start: 0.8930 (tmm) cc_final: 0.8632 (tmm) REVERT: J 75 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8944 (tmtm) REVERT: J 106 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7917 (mt-10) REVERT: J 118 GLU cc_start: 0.8391 (tt0) cc_final: 0.8058 (tp30) REVERT: K 1 MET cc_start: 0.7338 (mmm) cc_final: 0.6605 (mmm) REVERT: K 3 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: K 76 HIS cc_start: 0.7378 (m-70) cc_final: 0.6723 (p-80) REVERT: L 123 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6807 (tt0) REVERT: L 138 ASP cc_start: 0.7597 (m-30) cc_final: 0.7360 (m-30) REVERT: L 139 TYR cc_start: 0.7640 (m-80) cc_final: 0.7062 (p90) REVERT: L 205 GLN cc_start: 0.7913 (pm20) cc_final: 0.7412 (pm20) REVERT: L 244 LYS cc_start: 0.8114 (mttt) cc_final: 0.7765 (mmtp) REVERT: L 249 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7811 (mp0) REVERT: M 326 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7276 (ttmt) REVERT: N 64 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7974 (tp30) REVERT: O 56 ARG cc_start: 0.7657 (tmm160) cc_final: 0.7374 (mtm110) REVERT: O 215 LYS cc_start: 0.7892 (mttt) cc_final: 0.7527 (mptt) REVERT: O 248 GLU cc_start: 0.6479 (mt-10) cc_final: 0.5327 (tp30) REVERT: P 90 LYS cc_start: 0.8765 (mtpt) cc_final: 0.8507 (mtmt) REVERT: P 175 ARG cc_start: 0.7884 (mmm160) cc_final: 0.7289 (mmt180) REVERT: P 183 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7150 (tp30) REVERT: P 204 GLU cc_start: 0.7923 (mp0) cc_final: 0.7568 (mp0) REVERT: P 205 ASN cc_start: 0.8247 (p0) cc_final: 0.7778 (p0) REVERT: P 214 ASN cc_start: 0.8306 (p0) cc_final: 0.8028 (m110) REVERT: Q 189 MET cc_start: 0.7519 (mtp) cc_final: 0.7048 (ttp) REVERT: Q 204 LYS cc_start: 0.8192 (tptm) cc_final: 0.7860 (tppt) REVERT: Q 210 LYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5629 (mppt) REVERT: R 54 GLN cc_start: 0.7970 (pt0) cc_final: 0.7357 (mm-40) REVERT: R 56 SER cc_start: 0.5670 (OUTLIER) cc_final: 0.5282 (p) REVERT: R 61 LYS cc_start: 0.8233 (mmmm) cc_final: 0.7967 (tppt) REVERT: R 210 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8183 (mt0) REVERT: R 213 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7412 (pt0) REVERT: S 233 MET cc_start: 0.6626 (mmt) cc_final: 0.6324 (mmt) REVERT: S 282 THR cc_start: 0.7860 (m) cc_final: 0.7449 (p) REVERT: S 313 GLU cc_start: 0.7264 (mp0) cc_final: 0.7055 (mp0) REVERT: S 327 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7993 (tp) REVERT: S 329 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8037 (mmm) REVERT: T 205 LYS cc_start: 0.8157 (ttmm) cc_final: 0.7898 (tmtt) REVERT: T 221 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.6055 (mt) REVERT: T 276 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8399 (ptt) REVERT: T 390 GLU cc_start: 0.4260 (OUTLIER) cc_final: 0.3747 (mm-30) REVERT: U 61 LYS cc_start: 0.7606 (mttt) cc_final: 0.7256 (mmtt) REVERT: U 204 GLN cc_start: 0.6310 (OUTLIER) cc_final: 0.5464 (tm130) REVERT: V 137 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8611 (m-80) REVERT: V 139 LYS cc_start: 0.8588 (tppp) cc_final: 0.8283 (tttt) REVERT: W 213 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: X 12 MET cc_start: 0.8931 (tmm) cc_final: 0.8631 (tmm) REVERT: X 75 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8972 (tmtm) REVERT: X 118 GLU cc_start: 0.8387 (tt0) cc_final: 0.8060 (tp30) REVERT: Y 1 MET cc_start: 0.7250 (mmm) cc_final: 0.6783 (mtm) REVERT: Y 76 HIS cc_start: 0.7389 (m-70) cc_final: 0.6769 (p-80) REVERT: Y 116 GLU cc_start: 0.7614 (pm20) cc_final: 0.7219 (pp20) REVERT: Z 123 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6815 (tt0) REVERT: Z 138 ASP cc_start: 0.7631 (m-30) cc_final: 0.7352 (m-30) REVERT: Z 139 TYR cc_start: 0.7680 (m-80) cc_final: 0.7077 (p90) REVERT: Z 205 GLN cc_start: 0.7909 (pm20) cc_final: 0.7406 (pm20) REVERT: Z 244 LYS cc_start: 0.8124 (mttt) cc_final: 0.7772 (mmtp) REVERT: Z 249 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7811 (mp0) REVERT: a 326 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7484 (ptmt) REVERT: b 64 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7976 (tp30) outliers start: 86 outliers final: 50 residues processed: 812 average time/residue: 1.8920 time to fit residues: 1868.0369 Evaluate side-chains 824 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 748 time to evaluate : 5.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 326 LYS Chi-restraints excluded: chain N residue 70 GLN Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain Q residue 210 LYS Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 213 GLU Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 329 MET Chi-restraints excluded: chain T residue 221 LEU Chi-restraints excluded: chain T residue 276 MET Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 390 GLU Chi-restraints excluded: chain U residue 204 GLN Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain W residue 213 GLU Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 168 LEU Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain a residue 257 GLU Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 389 optimal weight: 2.9990 chunk 522 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 452 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 491 optimal weight: 0.9990 chunk 205 optimal weight: 0.0010 chunk 504 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 HIS D 23 GLN E 328 HIS F 190 ASN G 65 ASN H 266 GLN K 72 GLN K 125 GLN L 291 GLN M 280 ASN M 303 ASN M 330 GLN N 70 GLN N 205 HIS P 140 ASN Q 186 HIS R 23 GLN S 328 HIS T 190 ASN V 266 GLN Y 72 GLN Y 125 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN a 180 ASN a 280 ASN a 303 ASN a 330 GLN b 70 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.103536 restraints weight = 55096.777| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.28 r_work: 0.2983 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 49860 Z= 0.159 Angle : 0.497 8.162 67458 Z= 0.265 Chirality : 0.041 0.149 7516 Planarity : 0.004 0.045 8744 Dihedral : 5.144 58.990 6964 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Rotamer: Outliers : 1.55 % Allowed : 19.02 % Favored : 79.43 % 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: 1.25 (0.10), residues: 6256 helix: 2.06 (0.11), residues: 2328 sheet: 0.29 (0.12), residues: 1566 loop : 0.08 (0.13), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Z 154 HIS 0.004 0.001 HIS N 74 PHE 0.014 0.001 PHE T 389 TYR 0.014 0.001 TYR P 116 ARG 0.005 0.000 ARG Z 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27489.84 seconds wall clock time: 488 minutes 11.65 seconds (29291.65 seconds total)