Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 01:04:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oht_12908/04_2023/7oht_12908.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oht_12908/04_2023/7oht_12908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oht_12908/04_2023/7oht_12908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oht_12908/04_2023/7oht_12908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oht_12908/04_2023/7oht_12908.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oht_12908/04_2023/7oht_12908.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.005 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1618 5.49 5 Mg 2 5.21 5 S 132 5.16 5 C 41502 2.51 5 N 13686 2.21 5 O 18710 1.98 5 H 59714 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B ASP 206": "OD1" <-> "OD2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B ASP 216": "OD1" <-> "OD2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C ARG 326": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 337": "OE1" <-> "OE2" Residue "C PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "D ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 177": "OE1" <-> "OE2" Residue "D PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D GLU 221": "OE1" <-> "OE2" Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 250": "OD1" <-> "OD2" Residue "D PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 29": "OE1" <-> "OE2" Residue "F ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 233": "OE1" <-> "OE2" Residue "F GLU 234": "OE1" <-> "OE2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 135": "OE1" <-> "OE2" Residue "H PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 171": "OD1" <-> "OD2" Residue "H ARG 173": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 15": "OE1" <-> "OE2" Residue "J GLU 25": "OE1" <-> "OE2" Residue "J ASP 28": "OD1" <-> "OD2" Residue "J GLU 38": "OE1" <-> "OE2" Residue "J ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 77": "OE1" <-> "OE2" Residue "J GLU 78": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 173": "OD1" <-> "OD2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 92": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O GLU 4": "OE1" <-> "OE2" Residue "O GLU 40": "OE1" <-> "OE2" Residue "O PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 166": "OE1" <-> "OE2" Residue "O TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 34": "OE1" <-> "OE2" Residue "S PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 57": "OE1" <-> "OE2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T GLU 94": "OE1" <-> "OE2" Residue "T PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "T ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 139": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ASP 56": "OD1" <-> "OD2" Residue "V ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ASP 89": "OD1" <-> "OD2" Residue "V TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 16": "OD1" <-> "OD2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W ARG 31": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 32": "OE1" <-> "OE2" Residue "W TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 46": "OD1" <-> "OD2" Residue "W ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 83": "OE1" <-> "OE2" Residue "W TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ASP 183": "OD1" <-> "OD2" Residue "W ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ASP 224": "OD1" <-> "OD2" Residue "W GLU 229": "OE1" <-> "OE2" Residue "b ASP 7": "OD1" <-> "OD2" Residue "b ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 55": "OE1" <-> "OE2" Residue "b GLU 59": "OE1" <-> "OE2" Residue "b ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ASP 83": "OD1" <-> "OD2" Residue "b TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 106": "OE1" <-> "OE2" Residue "b ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 144": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 151": "OE1" <-> "OE2" Residue "b ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ASP 164": "OD1" <-> "OD2" Residue "b PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 210": "OD1" <-> "OD2" Residue "b GLU 230": "OE1" <-> "OE2" Residue "b GLU 231": "OE1" <-> "OE2" Residue "b GLU 258": "OE1" <-> "OE2" Residue "b PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 265": "OE1" <-> "OE2" Residue "b PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 296": "OE1" <-> "OE2" Residue "b ASP 299": "OD1" <-> "OD2" Residue "b ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 307": "OE1" <-> "OE2" Residue "b GLU 316": "OE1" <-> "OE2" Residue "b GLU 325": "OE1" <-> "OE2" Residue "b ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 345": "OE1" <-> "OE2" Residue "b ASP 370": "OD1" <-> "OD2" Residue "b GLU 380": "OE1" <-> "OE2" Residue "b ASP 401": "OD1" <-> "OD2" Residue "b GLU 423": "OE1" <-> "OE2" Residue "b ASP 425": "OD1" <-> "OD2" Residue "b GLU 426": "OE1" <-> "OE2" Residue "b ASP 437": "OD1" <-> "OD2" Residue "b ASP 446": "OD1" <-> "OD2" Residue "b GLU 458": "OE1" <-> "OE2" Residue "b GLU 460": "OE1" <-> "OE2" Residue "b GLU 464": "OE1" <-> "OE2" Residue "b PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f GLU 33": "OE1" <-> "OE2" Residue "f ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m GLU 7": "OE1" <-> "OE2" Residue "m ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m GLU 14": "OE1" <-> "OE2" Residue "m GLU 27": "OE1" <-> "OE2" Residue "m PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m ASP 74": "OD1" <-> "OD2" Residue "m ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ASP 124": "OD1" <-> "OD2" Residue "m ASP 133": "OD1" <-> "OD2" Residue "m PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m GLU 172": "OE1" <-> "OE2" Residue "m PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m ASP 223": "OD1" <-> "OD2" Residue "m ARG 238": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m GLU 243": "OE1" <-> "OE2" Residue "m GLU 249": "OE1" <-> "OE2" Residue "m ASP 263": "OD1" <-> "OD2" Residue "m GLU 280": "OE1" <-> "OE2" Residue "m PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m ASP 312": "OD1" <-> "OD2" Residue "m GLU 349": "OE1" <-> "OE2" Residue "m PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m ASP 377": "OD1" <-> "OD2" Residue "m GLU 391": "OE1" <-> "OE2" Residue "m GLU 397": "OE1" <-> "OE2" Residue "m GLU 429": "OE1" <-> "OE2" Residue "m ARG 437": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m GLU 443": "OE1" <-> "OE2" Residue "m ARG 459": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r GLU 130": "OE1" <-> "OE2" Residue "r GLU 132": "OE1" <-> "OE2" Residue "r ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r GLU 159": "OE1" <-> "OE2" Residue "r PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r GLU 188": "OE1" <-> "OE2" Residue "r GLU 227": "OE1" <-> "OE2" Residue "r ARG 251": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r ASP 252": "OD1" <-> "OD2" Residue "u ARG 2": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "u ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ASP 25": "OD1" <-> "OD2" Residue "u GLU 28": "OE1" <-> "OE2" Residue "u ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u GLU 97": "OE1" <-> "OE2" Residue "u ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "v PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v GLU 70": "OE1" <-> "OE2" Residue "v ASP 112": "OD1" <-> "OD2" Residue "v PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v GLU 168": "OE1" <-> "OE2" Residue "v ASP 189": "OD1" <-> "OD2" Residue "v PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v ASP 243": "OD1" <-> "OD2" Residue "v ASP 270": "OD1" <-> "OD2" Residue "w TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "w ASP 35": "OD1" <-> "OD2" Residue "w ASP 40": "OD1" <-> "OD2" Residue "w ASP 94": "OD1" <-> "OD2" Residue "w ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "w ARG 128": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "w ASP 135": "OD1" <-> "OD2" Residue "w GLU 136": "OE1" <-> "OE2" Residue "w TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "w ASP 175": "OD1" <-> "OD2" Residue "w GLU 192": "OE1" <-> "OE2" Residue "x GLU 21": "OE1" <-> "OE2" Residue "x PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x ASP 40": "OD1" <-> "OD2" Residue "x ASP 43": "OD1" <-> "OD2" Residue "x ASP 90": "OD1" <-> "OD2" Residue "x TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x ASP 207": "OD1" <-> "OD2" Residue "x ASP 223": "OD1" <-> "OD2" Residue "x ASP 264": "OD1" <-> "OD2" Residue "x TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x ASP 340": "OD1" <-> "OD2" Residue "x GLU 350": "OE1" <-> "OE2" Residue "x GLU 358": "OE1" <-> "OE2" Residue "x GLU 361": "OE1" <-> "OE2" Residue "x ASP 379": "OD1" <-> "OD2" Residue "x PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x ASP 413": "OD1" <-> "OD2" Residue "x TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x ASP 423": "OD1" <-> "OD2" Residue "x ASP 465": "OD1" <-> "OD2" Residue "x GLU 488": "OE1" <-> "OE2" Residue "x TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "y PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "y GLU 32": "OE1" <-> "OE2" Residue "y TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "y PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "y GLU 41": "OE1" <-> "OE2" Residue "y ASP 44": "OD1" <-> "OD2" Residue "y ASP 78": "OD1" <-> "OD2" Residue "y GLU 80": "OE1" <-> "OE2" Residue "y ARG 85": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "y ASP 90": "OD1" <-> "OD2" Residue "y GLU 98": "OE1" <-> "OE2" Residue "y ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "y ASP 122": "OD1" <-> "OD2" Residue "y GLU 124": "OE1" <-> "OE2" Residue "y GLU 171": "OE1" <-> "OE2" Residue "y GLU 219": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 135365 Number of models: 1 Model: "" Number of chains: 30 Chain: "1" Number of atoms: 47732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1485, 47732 Classifications: {'RNA': 1485} Modifications used: {'3*END': 1, 'rna2p_pur': 180, 'rna2p_pyr': 134, 'rna3p_pur': 643, 'rna3p_pyr': 528} Link IDs: {'rna2p': 313, 'rna3p': 1171} Chain breaks: 39 Chain: "2" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 605 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 2, 'rna3p': 16} Chain breaks: 1 Chain: "3" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 3661 Classifications: {'RNA': 114} Modifications used: {'3*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 54, 'rna3p_pyr': 49} Link IDs: {'rna2p': 11, 'rna3p': 102} Chain breaks: 4 Chain: "B" Number of atoms: 5624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5624 Classifications: {'peptide': 350} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 337} Chain breaks: 2 Chain: "C" Number of atoms: 3813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3813 Classifications: {'peptide': 239} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 227} Chain breaks: 3 Chain: "D" Number of atoms: 4236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4236 Classifications: {'peptide': 265} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Chain: "E" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2338 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "F" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3647 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "H" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3105 Classifications: {'peptide': 191} Modifications used: {'NH3': 1} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 184} Chain: "J" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 2738 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "M" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2214 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "O" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3216 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "Q" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1357 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain breaks: 3 Chain: "S" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2913 Classifications: {'peptide': 171} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 161} Chain: "T" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1899 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 109} Chain breaks: 2 Chain: "V" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1880 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "W" Number of atoms: 3806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3806 Classifications: {'peptide': 234} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 222} Chain: "b" Number of atoms: 7406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 7406 Classifications: {'peptide': 453} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 429} Chain breaks: 1 Chain: "e" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 625 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain breaks: 1 Chain: "f" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1731 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "m" Number of atoms: 7069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 7069 Classifications: {'peptide': 433} Link IDs: {'CIS': 2, 'PTRANS': 22, 'TRANS': 408} Chain breaks: 2 Chain: "r" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3827 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "u" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1633 Classifications: {'peptide': 94} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Chain: "v" Number of atoms: 4323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 4323 Classifications: {'peptide': 263} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 249} Chain breaks: 1 Chain: "w" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2960 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 12, 'TRANS': 169} Chain breaks: 1 Chain: "x" Number of atoms: 7606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 7606 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 25, 'TRANS': 462} Chain breaks: 5 Chain: "y" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3398 Classifications: {'peptide': 225} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0BZW SG CYS u 6 167.925 104.634 57.217 1.00 84.26 S ATOM A0C18 SG CYS u 9 168.761 101.157 57.892 1.00 90.82 S ATOM A0CB4 SG CYS u 32 164.995 101.624 56.611 1.00 92.04 S Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N VAL O 3 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (13 atoms not shown) pdb=" HG3 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (12 atoms not shown) pdb=" HD3 PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (17 atoms not shown) pdb="HD13 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (10 atoms not shown) pdb=" HB3 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (5 atoms not shown) pdb=" HA3 GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (20 atoms not shown) pdb=" HZ3 LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (5 atoms not shown) pdb=" HA3 GLY O 13 " occ=0.50 residue: pdb=" N HIS O 14 " occ=0.50 ... (15 atoms not shown) pdb=" HE1 HIS O 14 " occ=0.50 ... (remaining 185 not shown) Time building chain proxies: 43.81, per 1000 atoms: 0.32 Number of scatterers: 135365 At special positions: 0 Unit cell: (224.399, 225.462, 228.653, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 132 16.00 P 1618 15.00 Mg 2 11.99 O 18710 8.00 N 13686 7.00 C 41502 6.00 H 59714 1.00 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: 90.57 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN u 201 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 9 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 32 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 6 " 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9676 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 57 sheets defined 38.2% alpha, 16.7% beta 436 base pairs and 704 stacking pairs defined. Time for finding SS restraints: 45.55 Creating SS restraints... Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.909A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 154 Processing helix chain 'B' and resid 187 through 198 removed outlier: 3.507A pdb=" N LYS B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 381 removed outlier: 3.519A pdb=" N LYS B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'C' and resid 24 through 28 Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 132 through 138 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 173 through 179 removed outlier: 4.044A pdb=" N SER C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.898A pdb=" N LYS C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 243 removed outlier: 3.586A pdb=" N HIS C 243 " --> pdb=" O PRO C 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 240 through 243' Processing helix chain 'C' and resid 252 through 263 removed outlier: 4.787A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 292 through 299 Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.552A pdb=" N LEU C 324 " --> pdb=" O ASN C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'D' and resid 11 through 15 Processing helix chain 'D' and resid 20 through 25 removed outlier: 4.130A pdb=" N GLU D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 Processing helix chain 'D' and resid 81 through 87 Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 113 Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.954A pdb=" N ARG D 179 " --> pdb=" O SER D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 200 Processing helix chain 'D' and resid 201 through 213 Processing helix chain 'D' and resid 215 through 222 removed outlier: 3.841A pdb=" N PHE D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 232 through 250 removed outlier: 3.869A pdb=" N GLU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 273 removed outlier: 3.839A pdb=" N LYS D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 288 Processing helix chain 'E' and resid 44 through 48 removed outlier: 3.590A pdb=" N ARG E 48 " --> pdb=" O GLY E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 102 through 107 removed outlier: 3.517A pdb=" N ALA E 107 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 151 removed outlier: 4.253A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'E' and resid 170 through 174 Processing helix chain 'F' and resid 25 through 72 Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 120 through 130 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 159 removed outlier: 3.829A pdb=" N LYS F 158 " --> pdb=" O LYS F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.845A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 202 removed outlier: 3.581A pdb=" N ALA F 198 " --> pdb=" O HIS F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 244 removed outlier: 4.484A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.879A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 120 removed outlier: 3.616A pdb=" N GLY H 119 " --> pdb=" O ASN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 164 Processing helix chain 'J' and resid 27 through 42 Processing helix chain 'J' and resid 74 through 87 removed outlier: 3.917A pdb=" N GLU J 78 " --> pdb=" O PRO J 74 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL J 86 " --> pdb=" O ARG J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 112 Processing helix chain 'J' and resid 136 through 141 Processing helix chain 'J' and resid 155 through 166 removed outlier: 3.582A pdb=" N LYS J 166 " --> pdb=" O TRP J 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 97 removed outlier: 3.619A pdb=" N LYS M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 112 removed outlier: 3.648A pdb=" N ALA M 111 " --> pdb=" O GLU M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 135 Processing helix chain 'O' and resid 15 through 28 Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.509A pdb=" N PHE O 57 " --> pdb=" O LYS O 53 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS O 60 " --> pdb=" O ASP O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 88 removed outlier: 3.693A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 101 removed outlier: 3.723A pdb=" N ARG O 101 " --> pdb=" O ALA O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 145 Processing helix chain 'O' and resid 149 through 186 removed outlier: 3.569A pdb=" N LEU O 156 " --> pdb=" O VAL O 152 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 197 Processing helix chain 'Q' and resid 23 through 41 Processing helix chain 'Q' and resid 42 through 48 removed outlier: 3.983A pdb=" N VAL Q 48 " --> pdb=" O PHE Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 126 through 131 Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.527A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 115 Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'S' and resid 143 through 145 No H-bonds generated for 'chain 'S' and resid 143 through 145' Processing helix chain 'T' and resid 100 through 120 removed outlier: 4.274A pdb=" N GLU T 104 " --> pdb=" O LYS T 100 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE T 105 " --> pdb=" O CYS T 101 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS T 120 " --> pdb=" O ARG T 116 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 126 removed outlier: 3.616A pdb=" N LEU V 125 " --> pdb=" O GLU V 121 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 132 Processing helix chain 'W' and resid 19 through 37 removed outlier: 3.898A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 60 removed outlier: 3.589A pdb=" N TRP W 60 " --> pdb=" O ILE W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 80 through 84 removed outlier: 3.620A pdb=" N GLU W 84 " --> pdb=" O ARG W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 89 through 96 Processing helix chain 'W' and resid 108 through 119 Processing helix chain 'W' and resid 158 through 160 No H-bonds generated for 'chain 'W' and resid 158 through 160' Processing helix chain 'W' and resid 161 through 168 Processing helix chain 'W' and resid 196 through 207 Processing helix chain 'b' and resid 4 through 8 removed outlier: 4.397A pdb=" N ASP b 7 " --> pdb=" O SER b 4 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 28 Processing helix chain 'b' and resid 38 through 68 removed outlier: 3.638A pdb=" N PHE b 68 " --> pdb=" O ILE b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 87 Processing helix chain 'b' and resid 87 through 117 Processing helix chain 'b' and resid 121 through 142 removed outlier: 3.515A pdb=" N LYS b 142 " --> pdb=" O THR b 138 " (cutoff:3.500A) Processing helix chain 'b' and resid 143 through 158 Processing helix chain 'b' and resid 179 through 188 Processing helix chain 'b' and resid 233 through 246 Processing helix chain 'b' and resid 263 through 275 Processing helix chain 'b' and resid 276 through 279 removed outlier: 3.701A pdb=" N ALA b 279 " --> pdb=" O PRO b 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 276 through 279' Processing helix chain 'b' and resid 289 through 293 removed outlier: 3.621A pdb=" N ILE b 292 " --> pdb=" O LYS b 289 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 312 removed outlier: 3.962A pdb=" N VAL b 312 " --> pdb=" O SER b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 325 through 346 removed outlier: 4.025A pdb=" N MET b 329 " --> pdb=" O GLU b 325 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU b 330 " --> pdb=" O GLU b 326 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN b 346 " --> pdb=" O SER b 342 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 Processing helix chain 'b' and resid 399 through 407 Processing helix chain 'b' and resid 408 through 411 removed outlier: 3.503A pdb=" N VAL b 411 " --> pdb=" O GLY b 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 408 through 411' Processing helix chain 'b' and resid 425 through 429 removed outlier: 3.538A pdb=" N LYS b 428 " --> pdb=" O ASP b 425 " (cutoff:3.500A) Processing helix chain 'b' and resid 440 through 444 Processing helix chain 'b' and resid 448 through 452 Processing helix chain 'b' and resid 453 through 465 removed outlier: 3.814A pdb=" N GLU b 457 " --> pdb=" O LEU b 453 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU b 458 " --> pdb=" O GLN b 454 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 84 removed outlier: 3.549A pdb=" N THR e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 115 removed outlier: 4.312A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA e 110 " --> pdb=" O VAL e 106 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG e 111 " --> pdb=" O VAL e 107 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 42 Processing helix chain 'f' and resid 43 through 45 No H-bonds generated for 'chain 'f' and resid 43 through 45' Processing helix chain 'f' and resid 90 through 94 removed outlier: 3.547A pdb=" N PHE f 94 " --> pdb=" O ALA f 91 " (cutoff:3.500A) Processing helix chain 'm' and resid 6 through 15 removed outlier: 3.530A pdb=" N ARG m 10 " --> pdb=" O LYS m 6 " (cutoff:3.500A) Processing helix chain 'm' and resid 16 through 23 removed outlier: 5.896A pdb=" N ASN m 21 " --> pdb=" O LYS m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 32 through 41 removed outlier: 3.837A pdb=" N PHE m 38 " --> pdb=" O LYS m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 99 removed outlier: 3.558A pdb=" N LEU m 89 " --> pdb=" O SER m 85 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN m 90 " --> pdb=" O GLN m 86 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS m 91 " --> pdb=" O ASP m 87 " (cutoff:3.500A) Processing helix chain 'm' and resid 114 through 119 Processing helix chain 'm' and resid 130 through 135 removed outlier: 3.906A pdb=" N THR m 134 " --> pdb=" O ARG m 130 " (cutoff:3.500A) Processing helix chain 'm' and resid 136 through 141 Processing helix chain 'm' and resid 156 through 175 removed outlier: 3.532A pdb=" N LEU m 160 " --> pdb=" O ASN m 156 " (cutoff:3.500A) Processing helix chain 'm' and resid 200 through 204 Processing helix chain 'm' and resid 208 through 222 removed outlier: 5.309A pdb=" N LEU m 215 " --> pdb=" O ILE m 211 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TYR m 216 " --> pdb=" O TRP m 212 " (cutoff:3.500A) Processing helix chain 'm' and resid 239 through 250 removed outlier: 4.299A pdb=" N GLU m 243 " --> pdb=" O CYS m 239 " (cutoff:3.500A) Processing helix chain 'm' and resid 261 through 265 Processing helix chain 'm' and resid 266 through 278 Processing helix chain 'm' and resid 295 through 310 Processing helix chain 'm' and resid 327 through 337 Processing helix chain 'm' and resid 378 through 383 Processing helix chain 'm' and resid 389 through 393 Processing helix chain 'm' and resid 395 through 401 removed outlier: 3.821A pdb=" N GLN m 398 " --> pdb=" O HIS m 395 " (cutoff:3.500A) Proline residue: m 401 - end of helix Processing helix chain 'm' and resid 402 through 407 removed outlier: 3.844A pdb=" N ARG m 406 " --> pdb=" O GLY m 402 " (cutoff:3.500A) Processing helix chain 'm' and resid 408 through 416 Processing helix chain 'm' and resid 424 through 436 Processing helix chain 'm' and resid 439 through 443 removed outlier: 4.037A pdb=" N GLU m 443 " --> pdb=" O LYS m 440 " (cutoff:3.500A) Processing helix chain 'm' and resid 445 through 460 Processing helix chain 'r' and resid 6 through 15 Processing helix chain 'r' and resid 17 through 41 removed outlier: 3.868A pdb=" N GLU r 21 " --> pdb=" O ARG r 17 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU r 22 " --> pdb=" O LEU r 18 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN r 40 " --> pdb=" O SER r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 74 removed outlier: 4.064A pdb=" N LYS r 74 " --> pdb=" O GLN r 70 " (cutoff:3.500A) Processing helix chain 'r' and resid 165 through 169 Processing helix chain 'r' and resid 174 through 178 Processing helix chain 'r' and resid 207 through 213 Processing helix chain 'r' and resid 248 through 252 Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 45 through 49 Processing helix chain 'u' and resid 52 through 59 Processing helix chain 'u' and resid 84 through 112 removed outlier: 4.619A pdb=" N LYS u 91 " --> pdb=" O ALA u 87 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA u 92 " --> pdb=" O THR u 88 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET u 93 " --> pdb=" O THR u 89 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET u 112 " --> pdb=" O TYR u 108 " (cutoff:3.500A) Processing helix chain 'v' and resid 10 through 20 Processing helix chain 'v' and resid 39 through 52 Processing helix chain 'v' and resid 72 through 83 Processing helix chain 'v' and resid 146 through 151 Processing helix chain 'v' and resid 151 through 166 Processing helix chain 'v' and resid 176 through 178 No H-bonds generated for 'chain 'v' and resid 176 through 178' Processing helix chain 'v' and resid 241 through 249 Processing helix chain 'v' and resid 267 through 269 No H-bonds generated for 'chain 'v' and resid 267 through 269' Processing helix chain 'w' and resid 35 through 40 removed outlier: 3.631A pdb=" N ASP w 40 " --> pdb=" O LYS w 36 " (cutoff:3.500A) Processing helix chain 'w' and resid 44 through 66 removed outlier: 4.388A pdb=" N GLU w 48 " --> pdb=" O ALA w 44 " (cutoff:3.500A) Processing helix chain 'w' and resid 112 through 121 removed outlier: 3.799A pdb=" N LYS w 116 " --> pdb=" O THR w 112 " (cutoff:3.500A) Processing helix chain 'w' and resid 149 through 157 removed outlier: 3.502A pdb=" N LYS w 153 " --> pdb=" O GLY w 149 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU w 154 " --> pdb=" O ALA w 150 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP w 155 " --> pdb=" O ASN w 151 " (cutoff:3.500A) Processing helix chain 'w' and resid 175 through 200 removed outlier: 3.872A pdb=" N LEU w 179 " --> pdb=" O ASP w 175 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG w 181 " --> pdb=" O ARG w 177 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS w 200 " --> pdb=" O ARG w 196 " (cutoff:3.500A) Processing helix chain 'x' and resid 9 through 18 Processing helix chain 'x' and resid 56 through 69 removed outlier: 3.659A pdb=" N LEU x 64 " --> pdb=" O LEU x 60 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN x 65 " --> pdb=" O GLU x 61 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN x 66 " --> pdb=" O GLU x 62 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU x 67 " --> pdb=" O LEU x 63 " (cutoff:3.500A) Processing helix chain 'x' and resid 239 through 243 Processing helix chain 'x' and resid 330 through 337 removed outlier: 3.548A pdb=" N ILE x 336 " --> pdb=" O TYR x 332 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY x 337 " --> pdb=" O ALA x 333 " (cutoff:3.500A) Processing helix chain 'x' and resid 348 through 365 Processing helix chain 'y' and resid 12 through 16 removed outlier: 3.972A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 12 through 16' Processing helix chain 'y' and resid 31 through 43 removed outlier: 4.337A pdb=" N TYR y 35 " --> pdb=" O SER y 31 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 134 Processing helix chain 'y' and resid 147 through 152 removed outlier: 3.729A pdb=" N TYR y 151 " --> pdb=" O LEU y 147 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 211 through 223 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 359 removed outlier: 5.355A pdb=" N LEU B 356 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASP B 59 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE B 215 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN B 279 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 282 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS B 325 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B 284 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 52 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ASP B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS B 50 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 100 through 106 removed outlier: 7.143A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 106 removed outlier: 7.143A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 151 through 152 removed outlier: 7.029A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL C 207 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 186 through 187 removed outlier: 3.525A pdb=" N THR C 200 " --> pdb=" O LYS C 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 50 through 56 removed outlier: 4.167A pdb=" N ALA D 76 " --> pdb=" O ILE D 64 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 183 through 184 removed outlier: 4.518A pdb=" N GLU D 189 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 38 through 41 removed outlier: 7.032A pdb=" N LEU E 64 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N HIS E 57 " --> pdb=" O THR E 62 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR E 62 " --> pdb=" O HIS E 57 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG E 77 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 74 through 77 removed outlier: 3.504A pdb=" N VAL F 77 " --> pdb=" O ARG T 139 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG T 139 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.425A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL F 86 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL F 134 " --> pdb=" O GLY F 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AB3, first strand: chain 'H' and resid 5 through 11 removed outlier: 3.880A pdb=" N THR H 44 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 19 through 20 removed outlier: 4.003A pdb=" N SER H 19 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS H 26 " --> pdb=" O SER H 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 132 through 136 removed outlier: 3.530A pdb=" N TYR H 86 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LYS H 87 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LYS H 184 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LYS H 89 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 93 " --> pdb=" O GLY H 178 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY H 178 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 100 through 103 removed outlier: 3.665A pdb=" N ARG H 124 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 69 through 70 removed outlier: 5.099A pdb=" N ILE J 14 " --> pdb=" O ASN J 132 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN J 132 " --> pdb=" O ILE J 14 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS J 16 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN J 20 " --> pdb=" O ASP J 126 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 14 through 15 removed outlier: 3.552A pdb=" N VAL M 15 " --> pdb=" O PHE S 150 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE S 150 " --> pdb=" O VAL M 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'M' and resid 56 through 59 removed outlier: 3.816A pdb=" N GLN M 56 " --> pdb=" O ILE M 46 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE M 46 " --> pdb=" O GLN M 56 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE M 58 " --> pdb=" O VAL M 44 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 6 through 10 Processing sheet with id=AC2, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AC3, first strand: chain 'Q' and resid 80 through 82 Processing sheet with id=AC4, first strand: chain 'S' and resid 58 through 63 removed outlier: 4.557A pdb=" N SER S 60 " --> pdb=" O ILE S 10 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE S 10 " --> pdb=" O SER S 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN S 62 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE S 29 " --> pdb=" O TYR S 7 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 88 through 96 removed outlier: 3.566A pdb=" N HIS S 88 " --> pdb=" O TYR S 81 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR S 81 " --> pdb=" O HIS S 88 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS S 73 " --> pdb=" O ASP S 96 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS S 125 " --> pdb=" O TRP S 78 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'T' and resid 83 through 92 removed outlier: 6.435A pdb=" N ILE T 75 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL T 64 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 9.433A pdb=" N ASN T 77 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N GLY T 62 " --> pdb=" O ASN T 77 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'V' and resid 17 through 18 Processing sheet with id=AC8, first strand: chain 'V' and resid 22 through 25 removed outlier: 6.754A pdb=" N ASN V 33 " --> pdb=" O LYS V 63 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS V 63 " --> pdb=" O ASN V 33 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 65 through 67 removed outlier: 4.340A pdb=" N GLY W 101 " --> pdb=" O LEU W 43 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N HIS W 44 " --> pdb=" O VAL W 217 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL W 217 " --> pdb=" O HIS W 44 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU W 229 " --> pdb=" O TYR W 220 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'W' and resid 121 through 123 Processing sheet with id=AD2, first strand: chain 'W' and resid 135 through 137 removed outlier: 6.595A pdb=" N PHE W 135 " --> pdb=" O VAL W 188 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR W 186 " --> pdb=" O ILE W 137 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'W' and resid 140 through 141 removed outlier: 3.515A pdb=" N GLY W 140 " --> pdb=" O ILE W 182 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE W 182 " --> pdb=" O GLY W 140 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'b' and resid 171 through 174 removed outlier: 7.449A pdb=" N VAL b 286 " --> pdb=" O VAL b 250 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TYR b 252 " --> pdb=" O VAL b 286 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN b 288 " --> pdb=" O TYR b 252 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N MET b 254 " --> pdb=" O ASN b 288 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'b' and resid 206 through 211 Processing sheet with id=AD6, first strand: chain 'f' and resid 9 through 18 removed outlier: 7.197A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR f 16 " --> pdb=" O VAL f 27 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL f 27 " --> pdb=" O TYR f 16 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N ARG f 18 " --> pdb=" O PRO f 25 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'm' and resid 105 through 109 removed outlier: 6.518A pdb=" N LYS v 271 " --> pdb=" O LEU m 108 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU v 264 " --> pdb=" O LEU v 272 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'm' and resid 284 through 285 removed outlier: 3.932A pdb=" N PHE m 320 " --> pdb=" O ILE m 365 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE m 362 " --> pdb=" O LEU m 358 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU m 358 " --> pdb=" O ILE m 362 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN m 354 " --> pdb=" O ASP m 366 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'r' and resid 134 through 137 removed outlier: 4.423A pdb=" N LYS r 148 " --> pdb=" O ILE r 137 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'r' and resid 181 through 185 removed outlier: 3.677A pdb=" N LEU r 195 " --> pdb=" O ALA r 182 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL r 184 " --> pdb=" O VAL r 193 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL r 193 " --> pdb=" O VAL r 184 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE r 197 " --> pdb=" O ASN r 224 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASN r 224 " --> pdb=" O ILE r 197 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA r 199 " --> pdb=" O GLU r 222 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE r 220 " --> pdb=" O LYS r 201 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N ALA r 257 " --> pdb=" O LYS r 181 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASN r 183 " --> pdb=" O ALA r 257 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU r 259 " --> pdb=" O ASN r 183 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR r 185 " --> pdb=" O LEU r 259 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'u' and resid 4 through 5 removed outlier: 4.295A pdb=" N TYR u 4 " --> pdb=" O CYS u 13 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'u' and resid 19 through 22 Processing sheet with id=AE4, first strand: chain 'v' and resid 57 through 59 removed outlier: 3.564A pdb=" N MET v 90 " --> pdb=" O ILE v 33 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP v 112 " --> pdb=" O ARG v 104 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N PHE v 106 " --> pdb=" O ILE v 110 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE v 110 " --> pdb=" O PHE v 106 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ARG v 236 " --> pdb=" O GLU v 115 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET v 117 " --> pdb=" O ILE v 234 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE v 234 " --> pdb=" O MET v 117 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'v' and resid 57 through 59 removed outlier: 3.564A pdb=" N MET v 90 " --> pdb=" O ILE v 33 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP v 112 " --> pdb=" O ARG v 104 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N PHE v 106 " --> pdb=" O ILE v 110 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE v 110 " --> pdb=" O PHE v 106 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ARG v 236 " --> pdb=" O GLU v 115 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET v 117 " --> pdb=" O ILE v 234 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE v 234 " --> pdb=" O MET v 117 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET v 140 " --> pdb=" O ILE v 182 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N MET v 184 " --> pdb=" O MET v 140 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N THR v 142 " --> pdb=" O MET v 184 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE v 186 " --> pdb=" O THR v 142 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLN v 144 " --> pdb=" O ILE v 186 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE v 141 " --> pdb=" O ALA w 28 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ASP w 30 " --> pdb=" O PHE v 141 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE v 143 " --> pdb=" O ASP w 30 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'v' and resid 172 through 174 removed outlier: 3.996A pdb=" N LEU w 89 " --> pdb=" O LYS w 71 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'x' and resid 43 through 44 removed outlier: 3.881A pdb=" N PHE x 36 " --> pdb=" O ASN x 44 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'x' and resid 43 through 44 removed outlier: 3.881A pdb=" N PHE x 36 " --> pdb=" O ASN x 44 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYS x 35 " --> pdb=" O LEU x 119 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TYR x 121 " --> pdb=" O LYS x 35 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLN x 37 " --> pdb=" O TYR x 121 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'x' and resid 146 through 151 removed outlier: 3.623A pdb=" N VAL x 160 " --> pdb=" O ALA x 150 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG x 169 " --> pdb=" O THR x 161 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA x 168 " --> pdb=" O LEU x 182 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE x 170 " --> pdb=" O HIS x 180 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N HIS x 180 " --> pdb=" O ILE x 170 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ASP x 172 " --> pdb=" O PRO x 178 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'x' and resid 189 through 194 removed outlier: 3.581A pdb=" N CYS x 191 " --> pdb=" O GLY x 204 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'x' and resid 232 through 237 removed outlier: 6.710A pdb=" N SER x 254 " --> pdb=" O THR x 233 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU x 235 " --> pdb=" O ALA x 252 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA x 252 " --> pdb=" O LEU x 235 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET x 274 " --> pdb=" O ILE x 260 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE x 262 " --> pdb=" O TYR x 272 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR x 272 " --> pdb=" O ILE x 262 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'x' and resid 281 through 286 removed outlier: 3.724A pdb=" N CYS x 283 " --> pdb=" O GLY x 295 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER x 294 " --> pdb=" O ARG x 302 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG x 302 " --> pdb=" O SER x 294 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN x 314 " --> pdb=" O VAL x 303 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP x 305 " --> pdb=" O CYS x 312 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N CYS x 312 " --> pdb=" O ASP x 305 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'x' and resid 323 through 328 removed outlier: 3.723A pdb=" N HIS x 325 " --> pdb=" O ALA x 377 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR x 382 " --> pdb=" O SER x 378 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA x 396 " --> pdb=" O LEU x 385 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'x' and resid 405 through 410 removed outlier: 3.527A pdb=" N VAL x 418 " --> pdb=" O ALA x 409 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ASP x 430 " --> pdb=" O PHE x 436 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE x 436 " --> pdb=" O ASP x 430 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'x' and resid 447 through 452 removed outlier: 4.599A pdb=" N GLN x 449 " --> pdb=" O CYS x 462 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS x 462 " --> pdb=" O GLN x 449 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER x 463 " --> pdb=" O THR x 467 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR x 467 " --> pdb=" O SER x 463 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL x 480 " --> pdb=" O VAL x 470 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASP x 472 " --> pdb=" O LEU x 478 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU x 478 " --> pdb=" O ASP x 472 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'x' and resid 491 through 494 Processing sheet with id=AF8, first strand: chain 'y' and resid 3 through 4 removed outlier: 6.809A pdb=" N ALA y 204 " --> pdb=" O THR y 3 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'y' and resid 17 through 19 removed outlier: 6.733A pdb=" N CYS y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'y' and resid 64 through 65 Processing sheet with id=AG2, first strand: chain 'y' and resid 109 through 110 removed outlier: 3.507A pdb=" N VAL y 117 " --> pdb=" O PHE y 138 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'y' and resid 159 through 160 removed outlier: 6.739A pdb=" N GLY y 159 " --> pdb=" O VAL y 182 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 1602 hydrogen bonds defined for protein. 4461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1085 hydrogen bonds 1774 hydrogen bond angles 0 basepair planarities 436 basepair parallelities 704 stacking parallelities Total time for adding SS restraints: 71.88 Time building geometry restraints manager: 95.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 59668 1.03 - 1.23: 630 1.23 - 1.43: 38217 1.43 - 1.62: 41470 1.62 - 1.82: 217 Bond restraints: 140202 Sorted by residual: bond pdb=" N GLY m 2 " pdb=" CA GLY m 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.32e+00 bond pdb=" N LEU w 9 " pdb=" CA LEU w 9 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.32e+00 bond pdb=" N ASP Q 22 " pdb=" CA ASP Q 22 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N ASN e 78 " pdb=" CA ASN e 78 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N GLN J 6 " pdb=" CA GLN J 6 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 ... (remaining 140197 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.20: 11183 107.20 - 113.93: 156859 113.93 - 120.66: 49616 120.66 - 127.39: 31635 127.39 - 134.12: 3507 Bond angle restraints: 252800 Sorted by residual: angle pdb=" O3' A 11355 " pdb=" C3' A 11355 " pdb=" C2' A 11355 " ideal model delta sigma weight residual 109.50 114.94 -5.44 1.50e+00 4.44e-01 1.31e+01 angle pdb=" O3' C 12764 " pdb=" C3' C 12764 " pdb=" C2' C 12764 " ideal model delta sigma weight residual 109.50 114.90 -5.40 1.50e+00 4.44e-01 1.30e+01 angle pdb=" C PHE S 171 " pdb=" N TYR S 172 " pdb=" CA TYR S 172 " ideal model delta sigma weight residual 121.70 128.03 -6.33 1.80e+00 3.09e-01 1.24e+01 angle pdb=" OP1 U 13157 " pdb=" P U 13157 " pdb=" OP2 U 13157 " ideal model delta sigma weight residual 119.60 109.05 10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" C4' U 12860 " pdb=" C3' U 12860 " pdb=" O3' U 12860 " ideal model delta sigma weight residual 109.40 114.67 -5.27 1.50e+00 4.44e-01 1.23e+01 ... (remaining 252795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 53382 35.97 - 71.93: 1865 71.93 - 107.90: 253 107.90 - 143.87: 43 143.87 - 179.83: 52 Dihedral angle restraints: 55595 sinusoidal: 38360 harmonic: 17235 Sorted by residual: dihedral pdb=" C4' C 12764 " pdb=" C3' C 12764 " pdb=" C2' C 12764 " pdb=" C1' C 12764 " ideal model delta sinusoidal sigma weight residual -35.00 36.67 -71.67 1 8.00e+00 1.56e-02 1.03e+02 dihedral pdb=" C4' U 12860 " pdb=" C3' U 12860 " pdb=" C2' U 12860 " pdb=" C1' U 12860 " ideal model delta sinusoidal sigma weight residual -35.00 36.02 -71.02 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' A 12702 " pdb=" C3' A 12702 " pdb=" C2' A 12702 " pdb=" C1' A 12702 " ideal model delta sinusoidal sigma weight residual -35.00 35.81 -70.81 1 8.00e+00 1.56e-02 1.01e+02 ... (remaining 55592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 13512 0.066 - 0.132: 769 0.132 - 0.197: 21 0.197 - 0.263: 53 0.263 - 0.329: 11 Chirality restraints: 14366 Sorted by residual: chirality pdb=" C3' C 12764 " pdb=" C4' C 12764 " pdb=" O3' C 12764 " pdb=" C2' C 12764 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C3' C 13228 " pdb=" C4' C 13228 " pdb=" O3' C 13228 " pdb=" C2' C 13228 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" C3' U 12860 " pdb=" C4' U 12860 " pdb=" O3' U 12860 " pdb=" C2' U 12860 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 14363 not shown) Planarity restraints: 14870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS m 209 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C LYS m 209 " -0.067 2.00e-02 2.50e+03 pdb=" O LYS m 209 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG m 210 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 12857 " 0.035 2.00e-02 2.50e+03 2.26e-02 1.40e+01 pdb=" N1 C 12857 " -0.045 2.00e-02 2.50e+03 pdb=" C2 C 12857 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C 12857 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C 12857 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C 12857 " 0.041 2.00e-02 2.50e+03 pdb=" N4 C 12857 " -0.021 2.00e-02 2.50e+03 pdb=" C5 C 12857 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C 12857 " -0.004 2.00e-02 2.50e+03 pdb=" H5 C 12857 " 0.006 2.00e-02 2.50e+03 pdb=" H6 C 12857 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 11239 " 0.000 2.00e-02 2.50e+03 2.21e-02 1.34e+01 pdb=" N1 C 11239 " 0.003 2.00e-02 2.50e+03 pdb=" C2 C 11239 " 0.060 2.00e-02 2.50e+03 pdb=" O2 C 11239 " -0.035 2.00e-02 2.50e+03 pdb=" N3 C 11239 " -0.020 2.00e-02 2.50e+03 pdb=" C4 C 11239 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C 11239 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C 11239 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C 11239 " 0.000 2.00e-02 2.50e+03 pdb=" H5 C 11239 " -0.006 2.00e-02 2.50e+03 pdb=" H6 C 11239 " -0.008 2.00e-02 2.50e+03 ... (remaining 14867 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 2336 2.06 - 2.70: 189333 2.70 - 3.33: 373634 3.33 - 3.97: 486488 3.97 - 4.60: 747108 Nonbonded interactions: 1798899 Sorted by model distance: nonbonded pdb=" OP1 C 13018 " pdb="HD21 ASN y 9 " model vdw 1.430 1.850 nonbonded pdb=" O ASN r 4 " pdb=" H TYR r 6 " model vdw 1.498 1.850 nonbonded pdb=" OP1 G 13366 " pdb="HH12 ARG u 111 " model vdw 1.505 1.850 nonbonded pdb=" OP1 U 1 594 " pdb=" H1 G 1 609 " model vdw 1.536 1.850 nonbonded pdb=" O LYS m 209 " pdb=" H TRP m 212 " model vdw 1.540 1.850 ... (remaining 1798894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.290 Extract box with map and model: 21.710 Check model and map are aligned: 1.510 Set scattering table: 0.900 Process input model: 407.170 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 439.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 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 : 0.002 0.045 80488 Z= 0.106 Angle : 0.482 10.548 116485 Z= 0.246 Chirality : 0.035 0.329 14366 Planarity : 0.002 0.039 8780 Dihedral : 17.512 179.833 35287 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.30 % Favored : 94.60 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.83 (0.13), residues: 5054 helix: 2.65 (0.14), residues: 1612 sheet: 0.25 (0.20), residues: 664 loop : -0.67 (0.12), residues: 2778 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 542 time to evaluate : 6.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 27 residues processed: 596 average time/residue: 1.7003 time to fit residues: 1660.7583 Evaluate side-chains 390 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 363 time to evaluate : 6.503 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 3 residues processed: 27 average time/residue: 1.7074 time to fit residues: 82.4895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 561 optimal weight: 20.0000 chunk 504 optimal weight: 20.0000 chunk 279 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 339 optimal weight: 8.9990 chunk 269 optimal weight: 9.9990 chunk 521 optimal weight: 10.0000 chunk 201 optimal weight: 30.0000 chunk 316 optimal weight: 9.9990 chunk 387 optimal weight: 30.0000 chunk 603 optimal weight: 20.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS ** F 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 ASN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN M 119 GLN M 126 GLN O 29 ASN O 42 ASN ** T 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 327 ASN ** b 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 104 ASN f 42 GLN m 86 GLN ** m 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 260 ASN m 276 HIS m 455 ASN r 13 GLN r 14 HIS ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 9 ASN v 61 ASN v 64 ASN ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 297 HIS ** x 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.127 80488 Z= 0.347 Angle : 0.712 13.840 116485 Z= 0.374 Chirality : 0.038 0.315 14366 Planarity : 0.005 0.090 8780 Dihedral : 17.110 179.660 24910 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.66 % Favored : 92.16 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.44 (0.12), residues: 5054 helix: 1.25 (0.13), residues: 1649 sheet: -0.64 (0.17), residues: 778 loop : -1.20 (0.12), residues: 2627 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 408 time to evaluate : 6.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 414 average time/residue: 1.7316 time to fit residues: 1161.0658 Evaluate side-chains 328 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 326 time to evaluate : 6.107 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.1462 time to fit residues: 11.4664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 335 optimal weight: 9.9990 chunk 187 optimal weight: 20.0000 chunk 502 optimal weight: 30.0000 chunk 411 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 604 optimal weight: 20.0000 chunk 653 optimal weight: 20.0000 chunk 538 optimal weight: 10.0000 chunk 599 optimal weight: 8.9990 chunk 206 optimal weight: 40.0000 chunk 485 optimal weight: 20.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 GLN J 95 ASN ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 ASN T 54 HIS ** T 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 ASN ** b 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 104 ASN m 28 ASN ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 325 ASN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 7 HIS ** v 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 44 ASN ** x 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 80488 Z= 0.260 Angle : 0.587 8.569 116485 Z= 0.314 Chirality : 0.035 0.283 14366 Planarity : 0.004 0.051 8780 Dihedral : 17.384 179.059 24910 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.62 % Favored : 92.26 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.60 (0.12), residues: 5054 helix: 1.19 (0.13), residues: 1663 sheet: -0.79 (0.18), residues: 782 loop : -1.35 (0.12), residues: 2609 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 364 time to evaluate : 6.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 367 average time/residue: 1.7184 time to fit residues: 1029.6510 Evaluate side-chains 310 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 308 time to evaluate : 6.546 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.1788 time to fit residues: 11.6028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 597 optimal weight: 4.9990 chunk 454 optimal weight: 0.9990 chunk 313 optimal weight: 20.0000 chunk 66 optimal weight: 50.0000 chunk 288 optimal weight: 9.9990 chunk 406 optimal weight: 6.9990 chunk 607 optimal weight: 50.0000 chunk 642 optimal weight: 20.0000 chunk 317 optimal weight: 3.9990 chunk 575 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 45 ASN E 97 ASN ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 ASN J 101 ASN ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 104 ASN f 17 GLN ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 173 GLN w 57 ASN ** x 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 407 HIS ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 80488 Z= 0.168 Angle : 0.524 7.226 116485 Z= 0.276 Chirality : 0.034 0.277 14366 Planarity : 0.004 0.056 8780 Dihedral : 17.299 179.626 24910 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.64 % Favored : 92.22 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.33 (0.12), residues: 5054 helix: 1.51 (0.13), residues: 1662 sheet: -0.74 (0.17), residues: 791 loop : -1.23 (0.12), residues: 2601 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 6.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 361 average time/residue: 1.7114 time to fit residues: 1009.6166 Evaluate side-chains 311 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 310 time to evaluate : 6.516 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.1454 time to fit residues: 9.3201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 535 optimal weight: 7.9990 chunk 364 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 478 optimal weight: 20.0000 chunk 265 optimal weight: 0.5980 chunk 548 optimal weight: 20.0000 chunk 444 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 328 optimal weight: 9.9990 chunk 576 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 54 HIS ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 167 ASN e 104 ASN ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 26 ASN ** w 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 80488 Z= 0.229 Angle : 0.556 9.390 116485 Z= 0.295 Chirality : 0.035 0.344 14366 Planarity : 0.004 0.101 8780 Dihedral : 17.475 179.335 24910 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.31 % Favored : 91.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.59 (0.12), residues: 5054 helix: 1.25 (0.13), residues: 1665 sheet: -0.93 (0.18), residues: 789 loop : -1.33 (0.12), residues: 2600 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 6.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 1.6965 time to fit residues: 946.9660 Evaluate side-chains 295 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 6.544 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 216 optimal weight: 10.0000 chunk 578 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 377 optimal weight: 8.9990 chunk 158 optimal weight: 20.0000 chunk 643 optimal weight: 9.9990 chunk 534 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 chunk 337 optimal weight: 9.9990 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 HIS H 64 HIS H 77 ASN H 102 ASN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 104 ASN ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 165 ASN ** m 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 24 ASN ** w 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 68 ASN ** x 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 321 HIS ** x 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.189 80488 Z= 0.332 Angle : 0.694 9.480 116485 Z= 0.363 Chirality : 0.038 0.269 14366 Planarity : 0.005 0.145 8780 Dihedral : 18.326 178.913 24910 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 30.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.91 % Favored : 89.85 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.16 % Twisted Proline : 0.45 % Twisted General : 0.08 % 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: -1.36 (0.11), residues: 5054 helix: 0.40 (0.12), residues: 1681 sheet: -1.30 (0.17), residues: 760 loop : -1.67 (0.12), residues: 2613 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 6.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 1.7001 time to fit residues: 879.1519 Evaluate side-chains 264 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 6.536 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 620 optimal weight: 30.0000 chunk 72 optimal weight: 30.0000 chunk 366 optimal weight: 10.0000 chunk 469 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 541 optimal weight: 8.9990 chunk 359 optimal weight: 10.0000 chunk 640 optimal weight: 10.0000 chunk 401 optimal weight: 8.9990 chunk 390 optimal weight: 9.9990 chunk 295 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 HIS ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 HIS S 108 GLN ** T 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 78 HIS ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 406 ASN e 104 ASN m 80 ASN ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 411 HIS ** r 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 173 GLN ** w 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 401 HIS ** y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 80488 Z= 0.263 Angle : 0.614 11.741 116485 Z= 0.324 Chirality : 0.036 0.272 14366 Planarity : 0.005 0.067 8780 Dihedral : 18.382 179.659 24910 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.38 % Favored : 90.48 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.26 (0.12), residues: 5054 helix: 0.54 (0.13), residues: 1675 sheet: -1.27 (0.17), residues: 769 loop : -1.65 (0.12), residues: 2610 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 312 time to evaluate : 6.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 313 average time/residue: 1.6723 time to fit residues: 857.5344 Evaluate side-chains 273 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 6.575 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 396 optimal weight: 20.0000 chunk 255 optimal weight: 0.6980 chunk 382 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 407 optimal weight: 4.9990 chunk 436 optimal weight: 10.0000 chunk 316 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 503 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 104 ASN ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 325 ASN m 411 HIS ** r 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 449 GLN ** y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 80488 Z= 0.169 Angle : 0.542 8.990 116485 Z= 0.285 Chirality : 0.034 0.259 14366 Planarity : 0.004 0.094 8780 Dihedral : 18.176 179.652 24910 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.43 % Favored : 91.45 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.80 (0.12), residues: 5054 helix: 1.07 (0.13), residues: 1670 sheet: -1.13 (0.18), residues: 756 loop : -1.43 (0.12), residues: 2628 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 324 time to evaluate : 6.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 325 average time/residue: 1.6513 time to fit residues: 877.6691 Evaluate side-chains 278 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 6.566 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 583 optimal weight: 7.9990 chunk 614 optimal weight: 10.0000 chunk 560 optimal weight: 20.0000 chunk 597 optimal weight: 8.9990 chunk 613 optimal weight: 7.9990 chunk 359 optimal weight: 9.9990 chunk 260 optimal weight: 8.9990 chunk 469 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 539 optimal weight: 20.0000 chunk 564 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 104 ASN ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 411 HIS ** r 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 191 ASN ** w 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 79 GLN ** y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 80488 Z= 0.289 Angle : 0.626 9.273 116485 Z= 0.328 Chirality : 0.036 0.260 14366 Planarity : 0.005 0.067 8780 Dihedral : 18.476 179.582 24910 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 26.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.25 % Favored : 89.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.24 (0.12), residues: 5054 helix: 0.64 (0.13), residues: 1677 sheet: -1.43 (0.17), residues: 782 loop : -1.63 (0.12), residues: 2595 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 6.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 1.6140 time to fit residues: 804.0280 Evaluate side-chains 268 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 6.615 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 595 optimal weight: 7.9990 chunk 392 optimal weight: 8.9990 chunk 631 optimal weight: 3.9990 chunk 385 optimal weight: 10.0000 chunk 299 optimal weight: 6.9990 chunk 439 optimal weight: 10.0000 chunk 662 optimal weight: 20.0000 chunk 609 optimal weight: 5.9990 chunk 527 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 407 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 104 ASN ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 411 HIS ** r 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 402 GLN ** y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 145 ASN ** y 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 80488 Z= 0.209 Angle : 0.570 8.216 116485 Z= 0.300 Chirality : 0.035 0.247 14366 Planarity : 0.004 0.065 8780 Dihedral : 18.484 178.707 24910 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.28 % Favored : 90.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.12), residues: 5054 helix: 0.83 (0.13), residues: 1668 sheet: -1.33 (0.17), residues: 775 loop : -1.58 (0.12), residues: 2611 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10108 Ramachandran restraints generated. 5054 Oldfield, 0 Emsley, 5054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 6.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 1.6324 time to fit residues: 814.7457 Evaluate side-chains 264 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 6.649 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 323 optimal weight: 9.9990 chunk 419 optimal weight: 10.0000 chunk 561 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 486 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 chunk 528 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 542 optimal weight: 20.0000 chunk 66 optimal weight: 50.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 104 ASN ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 411 HIS ** r 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 66 GLN ** x 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 297 HIS ** y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 145 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.049981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.039590 restraints weight = 3363737.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.040578 restraints weight = 1670728.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.041229 restraints weight = 1060884.515| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.6581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 80488 Z= 0.237 Angle : 0.587 8.612 116485 Z= 0.309 Chirality : 0.035 0.415 14366 Planarity : 0.004 0.067 8780 Dihedral : 18.554 179.458 24910 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 24.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.93 % Favored : 89.91 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.12), residues: 5054 helix: 0.75 (0.13), residues: 1671 sheet: -1.44 (0.17), residues: 763 loop : -1.61 (0.12), residues: 2620 =============================================================================== Job complete usr+sys time: 27217.95 seconds wall clock time: 473 minutes 48.87 seconds (28428.87 seconds total)