Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 21 16:34:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/10_2023/8olu_16963_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/10_2023/8olu_16963.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/10_2023/8olu_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_16963/10_2023/8olu_16963_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/10_2023/8olu_16963_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/10_2023/8olu_16963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/10_2023/8olu_16963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/10_2023/8olu_16963_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/10_2023/8olu_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: 0.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 26.15, per 1000 atoms: 0.53 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: 19.56 Conformation dependent library (CDL) restraints added in 7.4 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: 7.24 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: 20.14 Time building geometry restraints manager: 21.13 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.750 Check model and map are aligned: 0.780 Set scattering table: 0.470 Process input model: 126.660 Find NCS groups from input model: 4.880 Set up NCS constraints: 0.470 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: 0.000 Load rotamer database and sin/cos tables:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.010 ------------------------------------------------------------------------------- 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 *********************** 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 : 5.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 309 outliers final: 81 residues processed: 1382 average time/residue: 1.8636 time to fit residues: 3125.8630 Evaluate side-chains 855 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 774 time to evaluate : 5.366 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 73 residues processed: 9 average time/residue: 0.4730 time to fit residues: 14.7744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 259 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 315 optimal weight: 0.9990 chunk 250 optimal weight: 0.9980 chunk 484 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 294 optimal weight: 0.9980 chunk 360 optimal weight: 3.9990 chunk 561 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 228 ASN A 236 ASN B 107 GLN B 140 ASN B 200 GLN C 239 HIS C 257 HIS D 23 GLN D 164 HIS E 222 GLN E 255 GLN E 262 HIS E 278 GLN E 288 ASN F 190 ASN F 331 GLN ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 HIS I 120 GLN I 201 GLN J 31 GLN J 65 ASN K 72 GLN K 102 GLN K 125 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 228 ASN P 107 GLN P 140 ASN P 200 GLN Q 239 HIS Q 257 HIS R 23 GLN R 164 HIS S 222 GLN S 255 GLN S 262 HIS S 278 GLN S 288 ASN T 190 ASN T 331 GLN ** V 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 115 HIS W 120 GLN W 201 GLN X 31 GLN X 65 ASN Y 72 GLN Y 102 GLN Y 125 GLN Y 186 ASN Z 108 ASN Z 291 GLN b 66 ASN b 70 GLN b 148 GLN b 205 HIS Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 49860 Z= 0.209 Angle : 0.623 7.524 67458 Z= 0.336 Chirality : 0.044 0.238 7516 Planarity : 0.005 0.066 8744 Dihedral : 5.839 57.770 6950 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.81 % Favored : 98.13 % Rotamer: Outliers : 3.43 % Allowed : 15.57 % Favored : 81.00 % 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: -0.20 (0.10), residues: 6256 helix: 0.47 (0.10), residues: 2310 sheet: 0.12 (0.13), residues: 1566 loop : -0.77 (0.12), residues: 2380 *********************** 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 1095 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 916 time to evaluate : 5.422 Fit side-chains outliers start: 179 outliers final: 69 residues processed: 1038 average time/residue: 1.8278 time to fit residues: 2313.6070 Evaluate side-chains 838 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 769 time to evaluate : 5.502 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 56 residues processed: 14 average time/residue: 0.6827 time to fit residues: 22.9186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 311 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 467 optimal weight: 10.0000 chunk 382 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 562 optimal weight: 9.9990 chunk 607 optimal weight: 6.9990 chunk 500 optimal weight: 4.9990 chunk 557 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 451 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN C 65 ASN D 23 GLN D 54 GLN D 223 GLN F 190 ASN F 206 ASN F 331 GLN ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN I 120 GLN I 166 GLN K 22 ASN L 291 GLN M 244 HIS M 280 ASN N 70 GLN N 205 HIS O 207 GLN P 93 GLN P 205 ASN Q 65 ASN R 23 GLN R 54 GLN R 223 GLN T 190 ASN T 206 ASN T 331 GLN ** V 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 266 GLN W 120 GLN W 166 GLN Y 72 GLN Y 76 HIS Z 291 GLN a 180 ASN a 244 HIS a 280 ASN a 303 ASN b 70 GLN b 94 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 49860 Z= 0.353 Angle : 0.642 8.464 67458 Z= 0.345 Chirality : 0.046 0.167 7516 Planarity : 0.005 0.055 8744 Dihedral : 5.759 58.225 6950 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.95 % Favored : 97.99 % Rotamer: Outliers : 3.80 % Allowed : 16.18 % Favored : 80.02 % 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: 0.40 (0.10), residues: 6256 helix: 1.13 (0.10), residues: 2324 sheet: 0.14 (0.12), residues: 1596 loop : -0.39 (0.12), residues: 2336 *********************** 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 1000 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 802 time to evaluate : 5.751 Fit side-chains outliers start: 198 outliers final: 93 residues processed: 936 average time/residue: 1.8323 time to fit residues: 2090.2250 Evaluate side-chains 833 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 740 time to evaluate : 5.249 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 72 residues processed: 21 average time/residue: 0.9920 time to fit residues: 36.0775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 555 optimal weight: 0.9980 chunk 422 optimal weight: 1.9990 chunk 291 optimal weight: 0.0000 chunk 62 optimal weight: 2.9990 chunk 268 optimal weight: 7.9990 chunk 377 optimal weight: 3.9990 chunk 564 optimal weight: 2.9990 chunk 597 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 chunk 534 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 GLN D 23 GLN D 54 GLN D 223 GLN F 190 ASN F 331 GLN ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 ASN H 266 GLN I 120 GLN I 247 GLN K 72 GLN K 76 HIS K 197 ASN L 291 GLN M 280 ASN M 303 ASN N 70 GLN N 205 HIS P 223 GLN R 23 GLN R 54 GLN R 164 HIS R 223 GLN T 190 ASN T 331 GLN U 204 GLN ** V 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 246 ASN V 266 GLN W 120 GLN W 247 GLN Y 22 ASN Y 72 GLN Z 291 GLN a 280 ASN a 303 ASN b 70 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 49860 Z= 0.256 Angle : 0.566 7.325 67458 Z= 0.303 Chirality : 0.043 0.149 7516 Planarity : 0.004 0.043 8744 Dihedral : 5.444 59.450 6950 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.61 % Favored : 98.35 % Rotamer: Outliers : 3.28 % Allowed : 16.78 % Favored : 79.95 % 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: 0.74 (0.10), residues: 6256 helix: 1.46 (0.11), residues: 2324 sheet: 0.26 (0.12), residues: 1586 loop : -0.21 (0.13), residues: 2346 *********************** 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 953 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 782 time to evaluate : 5.451 Fit side-chains outliers start: 171 outliers final: 93 residues processed: 904 average time/residue: 1.8316 time to fit residues: 2021.4291 Evaluate side-chains 836 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 743 time to evaluate : 5.569 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 77 residues processed: 16 average time/residue: 1.1814 time to fit residues: 32.6767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 497 optimal weight: 0.6980 chunk 339 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 444 optimal weight: 8.9990 chunk 246 optimal weight: 1.9990 chunk 509 optimal weight: 0.9990 chunk 412 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 305 optimal weight: 0.9990 chunk 536 optimal weight: 0.0970 chunk 150 optimal weight: 6.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 23 GLN D 164 HIS F 190 ASN H 211 GLN H 266 GLN I 120 GLN I 166 GLN K 72 GLN K 76 HIS L 291 GLN M 180 ASN M 244 HIS M 280 ASN M 303 ASN M 330 GLN N 66 ASN O 228 ASN R 23 GLN R 223 GLN T 190 ASN V 211 GLN V 266 GLN W 120 GLN Y 72 GLN Y 76 HIS ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN a 244 HIS a 280 ASN a 330 GLN b 66 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 49860 Z= 0.160 Angle : 0.500 6.886 67458 Z= 0.267 Chirality : 0.041 0.150 7516 Planarity : 0.004 0.042 8744 Dihedral : 4.970 57.527 6950 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.45 % Favored : 98.51 % Rotamer: Outliers : 2.63 % Allowed : 17.66 % Favored : 79.72 % 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: 1.87 (0.11), residues: 2312 sheet: 0.36 (0.12), residues: 1554 loop : -0.07 (0.13), residues: 2390 *********************** 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 968 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 831 time to evaluate : 5.807 Fit side-chains outliers start: 137 outliers final: 87 residues processed: 939 average time/residue: 1.8139 time to fit residues: 2091.7915 Evaluate side-chains 837 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 750 time to evaluate : 5.657 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 76 residues processed: 11 average time/residue: 0.7397 time to fit residues: 20.0650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 200 optimal weight: 4.9990 chunk 537 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 350 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 597 optimal weight: 0.7980 chunk 496 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 313 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN D 23 GLN E 113 ASN E 255 GLN E 328 HIS F 190 ASN F 331 GLN H 266 GLN K 72 GLN L 291 GLN M 180 ASN M 280 ASN M 303 ASN M 330 GLN O 228 ASN R 23 GLN S 113 ASN S 255 GLN S 328 HIS T 190 ASN V 266 GLN Y 72 GLN Y 76 HIS Z 291 GLN a 154 ASN a 280 ASN a 303 ASN a 330 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3218 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= 0.227 Angle : 0.530 7.183 67458 Z= 0.283 Chirality : 0.043 0.145 7516 Planarity : 0.004 0.044 8744 Dihedral : 5.098 57.529 6950 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.68 % Favored : 98.29 % Rotamer: Outliers : 2.63 % Allowed : 18.12 % Favored : 79.26 % 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: 1.07 (0.10), residues: 6256 helix: 1.82 (0.11), residues: 2324 sheet: 0.33 (0.12), residues: 1574 loop : -0.04 (0.13), residues: 2358 *********************** 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 894 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 757 time to evaluate : 5.391 Fit side-chains outliers start: 137 outliers final: 87 residues processed: 856 average time/residue: 1.8466 time to fit residues: 1935.9403 Evaluate side-chains 827 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 740 time to evaluate : 5.293 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 77 residues processed: 10 average time/residue: 1.0107 time to fit residues: 21.1384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 340 optimal weight: 1.9990 chunk 436 optimal weight: 4.9990 chunk 338 optimal weight: 7.9990 chunk 503 optimal weight: 0.0050 chunk 333 optimal weight: 4.9990 chunk 595 optimal weight: 2.9990 chunk 372 optimal weight: 0.6980 chunk 363 optimal weight: 3.9990 chunk 275 optimal weight: 0.6980 overall best weight: 1.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN C 30 GLN D 23 GLN E 113 ASN E 328 HIS F 190 ASN H 266 GLN K 72 GLN L 291 GLN M 180 ASN M 280 ASN M 303 ASN M 330 GLN R 23 GLN S 113 ASN T 190 ASN V 266 GLN Y 72 GLN Y 76 HIS Z 291 GLN 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: 0.8419 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 49860 Z= 0.206 Angle : 0.517 7.091 67458 Z= 0.276 Chirality : 0.042 0.146 7516 Planarity : 0.004 0.045 8744 Dihedral : 5.027 58.434 6950 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.73 % Favored : 98.24 % Rotamer: Outliers : 2.80 % Allowed : 18.19 % Favored : 79.01 % 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: 1.11 (0.10), residues: 6256 helix: 1.87 (0.11), residues: 2328 sheet: 0.33 (0.12), residues: 1580 loop : -0.00 (0.13), residues: 2348 *********************** 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: 146 poor density : 770 time to evaluate : 5.636 Fit side-chains outliers start: 146 outliers final: 94 residues processed: 884 average time/residue: 1.8938 time to fit residues: 2049.1496 Evaluate side-chains 856 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 762 time to evaluate : 6.032 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 84 residues processed: 10 average time/residue: 0.6322 time to fit residues: 17.6734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 368 optimal weight: 0.7980 chunk 237 optimal weight: 6.9990 chunk 355 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 115 optimal weight: 0.0770 chunk 378 optimal weight: 6.9990 chunk 405 optimal weight: 9.9990 chunk 294 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 468 optimal weight: 3.9990 overall best weight: 2.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 23 GLN E 113 ASN E 255 GLN E 328 HIS F 190 ASN G 65 ASN H 266 GLN K 72 GLN L 291 GLN M 180 ASN M 280 ASN M 330 GLN R 23 GLN S 113 ASN S 255 GLN S 328 HIS T 190 ASN U 65 ASN V 266 GLN Y 72 GLN Z 291 GLN a 280 ASN a 303 ASN a 330 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 49860 Z= 0.373 Angle : 0.613 7.555 67458 Z= 0.327 Chirality : 0.046 0.153 7516 Planarity : 0.005 0.046 8744 Dihedral : 5.473 57.273 6950 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.82 % Favored : 98.15 % Rotamer: Outliers : 2.78 % Allowed : 18.14 % Favored : 79.08 % 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: 0.84 (0.10), residues: 6256 helix: 1.59 (0.11), residues: 2330 sheet: 0.18 (0.12), residues: 1600 loop : -0.10 (0.13), residues: 2326 *********************** 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 872 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 727 time to evaluate : 5.398 Fit side-chains outliers start: 145 outliers final: 87 residues processed: 836 average time/residue: 1.8897 time to fit residues: 1921.6573 Evaluate side-chains 781 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 694 time to evaluate : 5.524 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 78 residues processed: 9 average time/residue: 0.9510 time to fit residues: 20.0615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 541 optimal weight: 0.9990 chunk 570 optimal weight: 0.9980 chunk 520 optimal weight: 0.9990 chunk 555 optimal weight: 1.9990 chunk 334 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 435 optimal weight: 0.8980 chunk 170 optimal weight: 0.5980 chunk 501 optimal weight: 4.9990 chunk 524 optimal weight: 0.0980 chunk 553 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 187 HIS C 186 HIS D 23 GLN E 113 ASN E 328 HIS F 190 ASN G 65 ASN H 266 GLN K 72 GLN K 76 HIS K 125 GLN M 180 ASN M 280 ASN M 303 ASN M 330 GLN N 70 GLN N 205 HIS Q 186 HIS R 23 GLN S 113 ASN S 328 HIS T 190 ASN U 65 ASN V 266 GLN Y 72 GLN Y 76 HIS ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 280 ASN a 303 ASN a 330 GLN b 70 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 49860 Z= 0.159 Angle : 0.501 6.967 67458 Z= 0.267 Chirality : 0.041 0.149 7516 Planarity : 0.004 0.045 8744 Dihedral : 4.958 58.711 6950 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.69 % Favored : 98.27 % Rotamer: Outliers : 1.99 % Allowed : 19.23 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.10), residues: 6256 helix: 1.91 (0.11), residues: 2324 sheet: 0.25 (0.12), residues: 1580 loop : 0.04 (0.13), residues: 2352 *********************** 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 884 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 780 time to evaluate : 5.966 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 86 residues processed: 871 average time/residue: 1.8346 time to fit residues: 1961.8164 Evaluate side-chains 823 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 737 time to evaluate : 5.694 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 82 residues processed: 6 average time/residue: 0.8256 time to fit residues: 15.2796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 364 optimal weight: 8.9990 chunk 586 optimal weight: 7.9990 chunk 358 optimal weight: 6.9990 chunk 278 optimal weight: 0.8980 chunk 408 optimal weight: 2.9990 chunk 615 optimal weight: 6.9990 chunk 566 optimal weight: 7.9990 chunk 490 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 378 optimal weight: 0.9990 chunk 300 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN B 187 HIS C 30 GLN C 186 HIS D 23 GLN E 113 ASN E 255 GLN E 328 HIS F 190 ASN G 65 ASN ** G 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN I 166 GLN K 72 GLN M 180 ASN M 280 ASN M 303 ASN M 330 GLN P 140 ASN P 187 HIS Q 186 HIS R 23 GLN S 113 ASN S 255 GLN S 328 HIS T 190 ASN U 65 ASN ** U 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 266 GLN W 166 GLN Y 72 GLN Y 76 HIS a 280 ASN a 303 ASN a 330 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 49860 Z= 0.220 Angle : 0.531 7.505 67458 Z= 0.283 Chirality : 0.042 0.149 7516 Planarity : 0.004 0.056 8744 Dihedral : 5.040 58.007 6950 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.71 % Favored : 98.26 % Rotamer: Outliers : 1.84 % Allowed : 19.73 % Favored : 78.43 % 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: 1.10 (0.10), residues: 6256 helix: 1.87 (0.11), residues: 2332 sheet: 0.25 (0.12), residues: 1590 loop : 0.03 (0.13), residues: 2334 ********************** 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 843 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 747 time to evaluate : 5.502 Fit side-chains outliers start: 96 outliers final: 83 residues processed: 831 average time/residue: 1.8214 time to fit residues: 1853.4962 Evaluate side-chains 813 residues out of total 5216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 730 time to evaluate : 5.505 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 80 residues processed: 5 average time/residue: 0.8693 time to fit residues: 13.7017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 389 optimal weight: 6.9990 chunk 522 optimal weight: 2.9990 chunk 150 optimal weight: 0.0570 chunk 452 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 491 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 504 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 140 ASN B 187 HIS C 186 HIS D 23 GLN E 113 ASN E 328 HIS F 190 ASN G 65 ASN ** G 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN K 72 GLN M 180 ASN M 280 ASN M 330 GLN O 228 ASN P 140 ASN P 187 HIS Q 30 GLN Q 186 HIS R 23 GLN S 113 ASN S 328 HIS T 190 ASN U 65 ASN ** U 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 266 GLN Y 72 GLN Y 76 HIS a 280 ASN a 303 ASN a 330 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.101809 restraints weight = 55065.467| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.18 r_work: 0.2961 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 49860 Z= 0.234 Angle : 0.540 8.135 67458 Z= 0.288 Chirality : 0.043 0.149 7516 Planarity : 0.004 0.066 8744 Dihedral : 5.091 58.395 6950 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Rotamer: Outliers : 1.92 % Allowed : 19.73 % Favored : 78.36 % 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: 1.07 (0.10), residues: 6256 helix: 1.84 (0.11), residues: 2328 sheet: 0.22 (0.12), residues: 1594 loop : 0.02 (0.13), residues: 2334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26754.78 seconds wall clock time: 472 minutes 8.13 seconds (28328.13 seconds total)