Starting phenix.real_space_refine on Sun Mar 17 03:19:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oht_12908/03_2024/7oht_12908.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oht_12908/03_2024/7oht_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_12908/03_2024/7oht_12908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oht_12908/03_2024/7oht_12908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oht_12908/03_2024/7oht_12908.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oht_12908/03_2024/7oht_12908.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 44.87, per 1000 atoms: 0.33 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: 85.41 Conformation dependent library (CDL) restraints added in 6.2 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: 44.97 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: 79.53 Time building geometry restraints manager: 90.48 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: 61586 35.97 - 71.93: 5297 71.93 - 107.90: 566 107.90 - 143.87: 43 143.87 - 179.83: 52 Dihedral angle restraints: 67544 sinusoidal: 50309 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 67541 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: 2.500 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: 1.240 Extract box with map and model: 17.160 Check model and map are aligned: 1.450 Set scattering table: 0.920 Process input model: 404.000 Find NCS groups from input model: 1.900 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: 0.020 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 431.740 ------------------------------------------------------------------------------- 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 : 22.766 179.833 40963 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 % Allowed : 13.18 % Favored : 85.54 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.000 TRP r 147 HIS 0.004 0.000 HIS J 109 PHE 0.007 0.000 PHE F 229 TYR 0.011 0.000 TYR b 91 ARG 0.007 0.000 ARG S 137 *********************** 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 : 5.991 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 REVERT: C 194 TYR cc_start: 0.6264 (m-80) cc_final: 0.6027 (m-80) REVERT: D 44 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.6848 (m-80) REVERT: E 155 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9278 (tt) REVERT: H 3 TYR cc_start: 0.8578 (m-80) cc_final: 0.8315 (m-80) REVERT: J 112 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6244 (pp) REVERT: M 121 MET cc_start: 0.8918 (ttp) cc_final: 0.8469 (ttt) REVERT: O 28 LEU cc_start: 0.8268 (mt) cc_final: 0.7803 (mm) REVERT: O 79 ILE cc_start: 0.8649 (mt) cc_final: 0.8373 (tp) REVERT: Q 126 GLN cc_start: 0.9237 (mt0) cc_final: 0.9029 (mp10) REVERT: S 94 ILE cc_start: 0.9239 (mt) cc_final: 0.8668 (pt) REVERT: S 162 THR cc_start: 0.8466 (p) cc_final: 0.7958 (p) REVERT: V 37 ILE cc_start: 0.8937 (pt) cc_final: 0.8469 (tt) REVERT: b 237 MET cc_start: 0.8732 (tpt) cc_final: 0.8419 (tpp) REVERT: f 30 ILE cc_start: 0.8694 (mm) cc_final: 0.8330 (tp) REVERT: m 411 HIS cc_start: 0.8143 (m-70) cc_final: 0.7818 (m170) outliers start: 57 outliers final: 27 residues processed: 596 average time/residue: 1.6865 time to fit residues: 1642.3833 Evaluate side-chains 396 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 366 time to evaluate : 6.038 ------------------------------------------------------------------------------- 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: 10.0000 chunk 279 optimal weight: 9.9990 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: 30.0000 overall best weight: 9.7992 ------------------------------------------------------------------------------- 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 J 43 GLN M 119 GLN M 126 GLN O 42 ASN ** 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 m 260 ASN m 276 HIS m 455 ASN r 13 GLN ** r 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 205 GLN ** 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** ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.147 80488 Z= 0.347 Angle : 0.676 11.800 116485 Z= 0.358 Chirality : 0.037 0.217 14366 Planarity : 0.005 0.093 8780 Dihedral : 23.847 179.864 30586 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.42 % Favored : 92.40 % Rotamer: Outliers : 0.09 % Allowed : 2.11 % Favored : 97.80 % 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: -0.27 (0.12), residues: 5054 helix: 1.41 (0.13), residues: 1654 sheet: -0.50 (0.18), residues: 762 loop : -1.13 (0.12), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP b 427 HIS 0.015 0.002 HIS x 228 PHE 0.024 0.002 PHE D 142 TYR 0.041 0.002 TYR Q 33 ARG 0.020 0.001 ARG b 135 *********************** 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 419 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 415 time to evaluate : 6.006 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: J 131 MET cc_start: 0.8509 (mmm) cc_final: 0.8088 (mpp) REVERT: M 22 LEU cc_start: 0.9195 (tp) cc_final: 0.8992 (tp) REVERT: M 121 MET cc_start: 0.9270 (ttp) cc_final: 0.8739 (ttt) REVERT: Q 126 GLN cc_start: 0.9217 (mt0) cc_final: 0.8908 (mp10) REVERT: S 147 ASP cc_start: 0.8650 (m-30) cc_final: 0.8228 (t0) REVERT: S 163 PHE cc_start: 0.8672 (m-80) cc_final: 0.8439 (m-80) REVERT: b 61 PHE cc_start: 0.9058 (m-80) cc_final: 0.8856 (m-10) REVERT: b 63 ASP cc_start: 0.8347 (m-30) cc_final: 0.8091 (m-30) REVERT: b 237 MET cc_start: 0.8879 (tpt) cc_final: 0.8655 (tpp) REVERT: b 318 MET cc_start: 0.8120 (mtm) cc_final: 0.7825 (ttt) REVERT: b 329 MET cc_start: 0.9342 (tpt) cc_final: 0.8897 (tpp) REVERT: f 30 ILE cc_start: 0.8667 (mm) cc_final: 0.8264 (tp) REVERT: m 411 HIS cc_start: 0.7967 (m-70) cc_final: 0.7585 (m170) REVERT: v 100 MET cc_start: 0.9343 (mmp) cc_final: 0.9040 (mmm) outliers start: 4 outliers final: 2 residues processed: 419 average time/residue: 1.6930 time to fit residues: 1146.2359 Evaluate side-chains 329 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 327 time to evaluate : 5.928 ------------------------------------------------------------------------------- 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: 10.0000 chunk 166 optimal weight: 7.9990 chunk 604 optimal weight: 6.9990 chunk 653 optimal weight: 20.0000 chunk 538 optimal weight: 9.9990 chunk 599 optimal weight: 7.9990 chunk 206 optimal weight: 40.0000 chunk 485 optimal weight: 20.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 95 ASN O 29 ASN O 50 ASN ** 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 88 ASN W 167 ASN ** b 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 104 ASN ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 17 GLN m 28 ASN ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 325 ASN r 13 GLN r 14 HIS ** 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** ** r 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 44 ASN ** x 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 407 HIS x 449 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 80488 Z= 0.288 Angle : 0.616 12.347 116485 Z= 0.328 Chirality : 0.036 0.269 14366 Planarity : 0.005 0.051 8780 Dihedral : 24.171 178.696 30586 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.87 % Favored : 92.01 % Rotamer: Outliers : 0.09 % Allowed : 2.36 % Favored : 97.55 % 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: -0.61 (0.12), residues: 5054 helix: 1.14 (0.13), residues: 1669 sheet: -0.84 (0.17), residues: 787 loop : -1.30 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP x 304 HIS 0.036 0.002 HIS x 297 PHE 0.055 0.002 PHE v 69 TYR 0.026 0.002 TYR m 257 ARG 0.024 0.001 ARG W 166 *********************** 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 363 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 359 time to evaluate : 5.543 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: D 49 TYR cc_start: 0.9025 (m-80) cc_final: 0.8771 (m-80) REVERT: H 5 GLN cc_start: 0.9073 (tp40) cc_final: 0.8605 (tm-30) REVERT: H 42 ASP cc_start: 0.8667 (t0) cc_final: 0.8399 (t0) REVERT: M 121 MET cc_start: 0.9321 (ttp) cc_final: 0.8967 (ttt) REVERT: Q 126 GLN cc_start: 0.9230 (mt0) cc_final: 0.8808 (mp10) REVERT: S 147 ASP cc_start: 0.8783 (m-30) cc_final: 0.8431 (t0) REVERT: S 163 PHE cc_start: 0.8691 (m-80) cc_final: 0.8414 (m-80) REVERT: T 139 ARG cc_start: 0.8305 (ptt-90) cc_final: 0.8052 (ptt-90) REVERT: b 16 ASP cc_start: 0.9370 (m-30) cc_final: 0.8965 (t0) REVERT: b 61 PHE cc_start: 0.9110 (m-80) cc_final: 0.8792 (m-10) REVERT: b 318 MET cc_start: 0.7946 (mtm) cc_final: 0.7694 (ttt) REVERT: b 329 MET cc_start: 0.9382 (tpt) cc_final: 0.8932 (tpp) REVERT: f 16 TYR cc_start: 0.7478 (m-80) cc_final: 0.7174 (m-80) REVERT: f 26 ASN cc_start: 0.8997 (t0) cc_final: 0.8728 (t0) REVERT: m 64 SER cc_start: 0.8683 (t) cc_final: 0.8313 (p) REVERT: m 411 HIS cc_start: 0.8174 (m-70) cc_final: 0.7846 (m90) REVERT: r 61 MET cc_start: 0.9060 (mmp) cc_final: 0.8847 (mmm) REVERT: r 65 ILE cc_start: 0.9521 (mt) cc_final: 0.9275 (tp) outliers start: 4 outliers final: 2 residues processed: 363 average time/residue: 1.7193 time to fit residues: 1014.4379 Evaluate side-chains 308 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 306 time to evaluate : 5.939 ------------------------------------------------------------------------------- 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: 9.9990 chunk 454 optimal weight: 4.9990 chunk 313 optimal weight: 20.0000 chunk 66 optimal weight: 50.0000 chunk 288 optimal weight: 10.0000 chunk 406 optimal weight: 0.6980 chunk 607 optimal weight: 40.0000 chunk 642 optimal weight: 20.0000 chunk 317 optimal weight: 3.9990 chunk 575 optimal weight: 20.0000 chunk 173 optimal weight: 7.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 ASN ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 104 ASN ** m 100 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** ** r 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 7 HIS ** v 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 ASN ** x 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 297 HIS ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 80488 Z= 0.199 Angle : 0.545 7.786 116485 Z= 0.289 Chirality : 0.034 0.277 14366 Planarity : 0.004 0.050 8780 Dihedral : 24.110 179.976 30586 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.68 % Favored : 92.16 % Rotamer: Outliers : 0.02 % Allowed : 1.30 % Favored : 98.68 % 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: -0.45 (0.12), residues: 5054 helix: 1.37 (0.13), residues: 1664 sheet: -0.84 (0.17), residues: 786 loop : -1.25 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP x 429 HIS 0.014 0.001 HIS x 297 PHE 0.043 0.002 PHE x 422 TYR 0.017 0.001 TYR J 116 ARG 0.028 0.000 ARG r 170 *********************** 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 356 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 6.014 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: D 49 TYR cc_start: 0.8966 (m-80) cc_final: 0.8716 (m-80) REVERT: H 5 GLN cc_start: 0.9053 (tp40) cc_final: 0.8590 (tm-30) REVERT: H 42 ASP cc_start: 0.8602 (t0) cc_final: 0.8220 (t0) REVERT: J 131 MET cc_start: 0.8577 (mmm) cc_final: 0.8316 (mpp) REVERT: M 121 MET cc_start: 0.9300 (ttp) cc_final: 0.8745 (ttp) REVERT: Q 126 GLN cc_start: 0.9251 (mt0) cc_final: 0.8850 (mp10) REVERT: S 147 ASP cc_start: 0.8819 (m-30) cc_final: 0.8496 (t0) REVERT: S 163 PHE cc_start: 0.8669 (m-80) cc_final: 0.8324 (m-80) REVERT: b 16 ASP cc_start: 0.9343 (m-30) cc_final: 0.8974 (t0) REVERT: b 61 PHE cc_start: 0.9019 (m-80) cc_final: 0.8666 (m-10) REVERT: b 318 MET cc_start: 0.7989 (mtm) cc_final: 0.7641 (mtp) REVERT: b 329 MET cc_start: 0.9341 (tpt) cc_final: 0.8894 (tpp) REVERT: m 64 SER cc_start: 0.8707 (t) cc_final: 0.8375 (p) REVERT: m 411 HIS cc_start: 0.8115 (m-70) cc_final: 0.7789 (m90) REVERT: r 61 MET cc_start: 0.9024 (mmp) cc_final: 0.8812 (mmm) REVERT: r 65 ILE cc_start: 0.9523 (mt) cc_final: 0.9263 (tp) outliers start: 1 outliers final: 1 residues processed: 356 average time/residue: 1.6926 time to fit residues: 987.6394 Evaluate side-chains 308 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 307 time to evaluate : 5.924 ------------------------------------------------------------------------------- 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: 2.9990 chunk 364 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 478 optimal weight: 40.0000 chunk 265 optimal weight: 1.9990 chunk 548 optimal weight: 20.0000 chunk 444 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 328 optimal weight: 10.0000 chunk 576 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 overall best weight: 5.9994 ------------------------------------------------------------------------------- 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** D 57 ASN ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN H 58 HIS H 64 HIS H 77 ASN ** J 101 ASN ** 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 205 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 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 80488 Z= 0.214 Angle : 0.546 10.454 116485 Z= 0.290 Chirality : 0.034 0.327 14366 Planarity : 0.004 0.091 8780 Dihedral : 24.149 178.956 30586 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.31 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: -0.55 (0.12), residues: 5054 helix: 1.30 (0.13), residues: 1656 sheet: -1.00 (0.17), residues: 800 loop : -1.28 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP x 513 HIS 0.008 0.001 HIS T 54 PHE 0.043 0.002 PHE y 34 TYR 0.028 0.001 TYR b 175 ARG 0.010 0.000 ARG b 400 *********************** 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 347 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 6.000 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: D 49 TYR cc_start: 0.8988 (m-80) cc_final: 0.8733 (m-80) REVERT: D 177 GLU cc_start: 0.9314 (pm20) cc_final: 0.8980 (mp0) REVERT: M 121 MET cc_start: 0.9305 (ttp) cc_final: 0.8781 (ttp) REVERT: Q 126 GLN cc_start: 0.9268 (mt0) cc_final: 0.8857 (mp10) REVERT: S 147 ASP cc_start: 0.8828 (m-30) cc_final: 0.8547 (t0) REVERT: S 163 PHE cc_start: 0.8691 (m-80) cc_final: 0.8381 (m-80) REVERT: b 16 ASP cc_start: 0.9338 (m-30) cc_final: 0.8975 (t0) REVERT: b 61 PHE cc_start: 0.9051 (m-80) cc_final: 0.8710 (m-10) REVERT: b 318 MET cc_start: 0.8030 (mtm) cc_final: 0.7698 (mtp) REVERT: b 329 MET cc_start: 0.9343 (tpt) cc_final: 0.8905 (tpp) REVERT: m 64 SER cc_start: 0.8736 (t) cc_final: 0.8413 (p) REVERT: m 411 HIS cc_start: 0.8161 (m-70) cc_final: 0.7848 (m90) REVERT: r 61 MET cc_start: 0.9062 (mmp) cc_final: 0.8839 (mmm) REVERT: r 65 ILE cc_start: 0.9498 (mt) cc_final: 0.9236 (tp) REVERT: w 140 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8399 (mm-30) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 1.6745 time to fit residues: 939.8557 Evaluate side-chains 302 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 5.946 ------------------------------------------------------------------------------- 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: 8.9990 chunk 578 optimal weight: 30.0000 chunk 127 optimal weight: 10.0000 chunk 377 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 643 optimal weight: 20.0000 chunk 534 optimal weight: 6.9990 chunk 297 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 212 optimal weight: 20.0000 chunk 337 optimal weight: 10.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- 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 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 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** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 78 HIS e 104 ASN ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 165 ASN ** r 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 24 ASN ** v 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 26 ASN ** w 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 142 HIS ** x 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 321 HIS x 449 GLN ** y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 80488 Z= 0.305 Angle : 0.645 9.142 116485 Z= 0.340 Chirality : 0.037 0.273 14366 Planarity : 0.005 0.060 8780 Dihedral : 24.470 179.757 30586 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 25.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.26 % Favored : 90.54 % Rotamer: Outliers : 0.04 % Allowed : 2.18 % Favored : 97.78 % 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: -1.09 (0.12), residues: 5054 helix: 0.71 (0.13), residues: 1679 sheet: -1.18 (0.18), residues: 759 loop : -1.55 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP x 322 HIS 0.014 0.002 HIS x 142 PHE 0.029 0.002 PHE x 151 TYR 0.055 0.002 TYR S 165 ARG 0.009 0.001 ARG r 178 *********************** 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 324 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 322 time to evaluate : 6.490 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: D 49 TYR cc_start: 0.9034 (m-80) cc_final: 0.8687 (m-80) REVERT: H 105 GLU cc_start: 0.9180 (pm20) cc_final: 0.8972 (pm20) REVERT: H 110 LYS cc_start: 0.9452 (mtmt) cc_final: 0.9244 (mtmm) REVERT: Q 126 GLN cc_start: 0.9267 (mt0) cc_final: 0.8797 (mp10) REVERT: S 17 GLU cc_start: 0.9454 (tp30) cc_final: 0.9228 (tp30) REVERT: S 147 ASP cc_start: 0.8870 (m-30) cc_final: 0.8663 (t0) REVERT: S 163 PHE cc_start: 0.8757 (m-80) cc_final: 0.8487 (m-80) REVERT: b 16 ASP cc_start: 0.9342 (m-30) cc_final: 0.8967 (t0) REVERT: b 61 PHE cc_start: 0.9040 (m-80) cc_final: 0.8753 (m-10) REVERT: b 254 MET cc_start: 0.8412 (mtt) cc_final: 0.7988 (mmm) REVERT: b 318 MET cc_start: 0.8193 (mtm) cc_final: 0.7797 (mtp) REVERT: b 329 MET cc_start: 0.9388 (tpt) cc_final: 0.8984 (tpp) REVERT: f 26 ASN cc_start: 0.9100 (t0) cc_final: 0.8895 (t0) REVERT: m 64 SER cc_start: 0.8789 (t) cc_final: 0.8464 (p) REVERT: m 144 LYS cc_start: 0.8347 (mmtt) cc_final: 0.7661 (mmmm) REVERT: m 411 HIS cc_start: 0.8260 (m-70) cc_final: 0.7906 (m90) REVERT: w 140 GLU cc_start: 0.9358 (mm-30) cc_final: 0.8708 (mm-30) outliers start: 2 outliers final: 0 residues processed: 323 average time/residue: 1.7064 time to fit residues: 897.2261 Evaluate side-chains 282 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 5.925 ------------------------------------------------------------------------------- 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: 6.9990 chunk 72 optimal weight: 30.0000 chunk 366 optimal weight: 9.9990 chunk 469 optimal weight: 9.9990 chunk 364 optimal weight: 9.9990 chunk 541 optimal weight: 20.0000 chunk 359 optimal weight: 9.9990 chunk 640 optimal weight: 1.9990 chunk 401 optimal weight: 20.0000 chunk 390 optimal weight: 10.0000 chunk 295 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** 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 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 HIS ** 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 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 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 142 HIS ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 80488 Z= 0.246 Angle : 0.591 8.078 116485 Z= 0.312 Chirality : 0.036 0.271 14366 Planarity : 0.004 0.056 8780 Dihedral : 24.551 179.931 30586 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.77 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -1.02 (0.12), residues: 5054 helix: 0.80 (0.13), residues: 1675 sheet: -1.25 (0.18), residues: 763 loop : -1.50 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP x 322 HIS 0.009 0.001 HIS x 401 PHE 0.026 0.002 PHE x 422 TYR 0.019 0.002 TYR D 265 ARG 0.010 0.001 ARG B 284 *********************** 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 319 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 5.995 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: D 49 TYR cc_start: 0.9053 (m-80) cc_final: 0.8807 (m-80) REVERT: H 42 ASP cc_start: 0.9010 (t0) cc_final: 0.8788 (t0) REVERT: Q 126 GLN cc_start: 0.9315 (mt0) cc_final: 0.8782 (mp10) REVERT: S 17 GLU cc_start: 0.9424 (tp30) cc_final: 0.9196 (tp30) REVERT: S 163 PHE cc_start: 0.8747 (m-80) cc_final: 0.8528 (m-80) REVERT: b 16 ASP cc_start: 0.9338 (m-30) cc_final: 0.8971 (t0) REVERT: b 61 PHE cc_start: 0.9040 (m-80) cc_final: 0.8781 (m-10) REVERT: b 318 MET cc_start: 0.8494 (mtm) cc_final: 0.8185 (mtp) REVERT: b 329 MET cc_start: 0.9364 (tpt) cc_final: 0.8944 (tpp) REVERT: f 26 ASN cc_start: 0.9135 (t0) cc_final: 0.8900 (t0) REVERT: m 64 SER cc_start: 0.8825 (t) cc_final: 0.8479 (p) REVERT: m 144 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7626 (mmmm) REVERT: m 411 HIS cc_start: 0.8283 (m-70) cc_final: 0.7941 (m90) REVERT: r 65 ILE cc_start: 0.9559 (mt) cc_final: 0.9253 (tp) REVERT: r 150 MET cc_start: 0.8351 (tmm) cc_final: 0.8088 (tmm) REVERT: w 140 GLU cc_start: 0.9441 (mm-30) cc_final: 0.8845 (mm-30) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 1.6383 time to fit residues: 846.3178 Evaluate side-chains 278 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 5.497 ------------------------------------------------------------------------------- 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: 9.9990 chunk 255 optimal weight: 10.0000 chunk 382 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 407 optimal weight: 8.9990 chunk 436 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 503 optimal weight: 20.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 HIS ** 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 100 ASN ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 HIS ** 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 127 GLN ** 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 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 104 ASN ** m 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 100 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 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 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 68 ASN ** x 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 80488 Z= 0.319 Angle : 0.677 12.965 116485 Z= 0.355 Chirality : 0.038 0.261 14366 Planarity : 0.005 0.114 8780 Dihedral : 24.807 179.021 30586 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 30.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.61 % Favored : 89.20 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: -1.46 (0.11), residues: 5054 helix: 0.42 (0.13), residues: 1679 sheet: -1.50 (0.17), residues: 776 loop : -1.76 (0.12), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP x 322 HIS 0.010 0.002 HIS r 14 PHE 0.027 0.002 PHE v 69 TYR 0.048 0.002 TYR x 381 ARG 0.015 0.001 ARG x 211 *********************** 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 306 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 5.971 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: D 44 TYR cc_start: 0.8106 (m-80) cc_final: 0.7388 (m-80) REVERT: Q 126 GLN cc_start: 0.9342 (mt0) cc_final: 0.8784 (mp10) REVERT: T 56 PHE cc_start: 0.8843 (p90) cc_final: 0.8618 (p90) REVERT: b 61 PHE cc_start: 0.8994 (m-80) cc_final: 0.8782 (m-10) REVERT: b 318 MET cc_start: 0.8553 (mtm) cc_final: 0.8012 (mtp) REVERT: m 64 SER cc_start: 0.8914 (t) cc_final: 0.8629 (p) REVERT: m 144 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7633 (mmmm) REVERT: m 411 HIS cc_start: 0.8336 (m170) cc_final: 0.8130 (m90) REVERT: r 230 MET cc_start: 0.8820 (ptp) cc_final: 0.8604 (tmm) REVERT: w 140 GLU cc_start: 0.9559 (mm-30) cc_final: 0.9017 (mm-30) REVERT: x 398 MET cc_start: 0.9384 (mpp) cc_final: 0.8959 (mpp) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 1.5685 time to fit residues: 782.5130 Evaluate side-chains 269 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 5.291 ------------------------------------------------------------------------------- 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: 6.9990 chunk 614 optimal weight: 10.0000 chunk 560 optimal weight: 30.0000 chunk 597 optimal weight: 0.6980 chunk 613 optimal weight: 5.9990 chunk 359 optimal weight: 10.0000 chunk 260 optimal weight: 8.9990 chunk 469 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 539 optimal weight: 10.0000 chunk 564 optimal weight: 20.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 108 GLN ** 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 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 267 GLN b 406 ASN 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 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 10 HIS ** 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 142 HIS ** 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.6285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 80488 Z= 0.185 Angle : 0.568 7.973 116485 Z= 0.299 Chirality : 0.035 0.240 14366 Planarity : 0.004 0.109 8780 Dihedral : 24.709 179.696 30586 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.67 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -1.03 (0.12), residues: 5054 helix: 0.86 (0.13), residues: 1672 sheet: -1.36 (0.18), residues: 749 loop : -1.52 (0.12), residues: 2633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP m 77 HIS 0.008 0.001 HIS x 142 PHE 0.027 0.002 PHE D 142 TYR 0.021 0.002 TYR D 49 ARG 0.009 0.001 ARG m 238 *********************** 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 314 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 6.010 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: D 44 TYR cc_start: 0.7909 (m-80) cc_final: 0.7161 (m-80) REVERT: H 42 ASP cc_start: 0.8995 (t0) cc_final: 0.8723 (t0) REVERT: Q 126 GLN cc_start: 0.9341 (mt0) cc_final: 0.8792 (mp10) REVERT: S 17 GLU cc_start: 0.9434 (tp30) cc_final: 0.9212 (tp30) REVERT: T 56 PHE cc_start: 0.8808 (p90) cc_final: 0.8605 (p90) REVERT: b 16 ASP cc_start: 0.9336 (m-30) cc_final: 0.8803 (t0) REVERT: b 61 PHE cc_start: 0.9000 (m-80) cc_final: 0.8798 (m-10) REVERT: b 318 MET cc_start: 0.8181 (mtm) cc_final: 0.7807 (mtp) REVERT: b 329 MET cc_start: 0.9362 (tpt) cc_final: 0.8963 (tpp) REVERT: m 64 SER cc_start: 0.8884 (t) cc_final: 0.8591 (p) REVERT: v 90 MET cc_start: 0.7864 (mpp) cc_final: 0.7554 (mpp) REVERT: w 140 GLU cc_start: 0.9485 (mm-30) cc_final: 0.8968 (mm-30) REVERT: x 398 MET cc_start: 0.9293 (mpp) cc_final: 0.8821 (mpp) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 1.5817 time to fit residues: 810.7658 Evaluate side-chains 269 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 5.400 ------------------------------------------------------------------------------- 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: 0.6980 chunk 392 optimal weight: 4.9990 chunk 631 optimal weight: 7.9990 chunk 385 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 chunk 439 optimal weight: 0.9980 chunk 662 optimal weight: 0.7980 chunk 609 optimal weight: 6.9990 chunk 527 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 407 optimal weight: 8.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 HIS ** 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 26 GLN 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 325 ASN ** r 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 24 ASN ** v 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 142 HIS ** x 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6838 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 80488 Z= 0.151 Angle : 0.528 7.891 116485 Z= 0.278 Chirality : 0.034 0.191 14366 Planarity : 0.004 0.107 8780 Dihedral : 24.447 179.317 30586 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.37 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: -0.67 (0.12), residues: 5054 helix: 1.21 (0.13), residues: 1667 sheet: -1.19 (0.18), residues: 762 loop : -1.33 (0.12), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP m 353 HIS 0.019 0.001 HIS S 49 PHE 0.021 0.001 PHE v 128 TYR 0.048 0.001 TYR r 242 ARG 0.008 0.000 ARG S 13 ********************** 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 319 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 5.985 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: D 44 TYR cc_start: 0.7887 (m-80) cc_final: 0.7196 (m-80) REVERT: H 42 ASP cc_start: 0.8934 (t0) cc_final: 0.8700 (t0) REVERT: H 64 HIS cc_start: 0.7528 (t-170) cc_final: 0.7325 (t-170) REVERT: J 131 MET cc_start: 0.8392 (mpp) cc_final: 0.8016 (mpp) REVERT: Q 126 GLN cc_start: 0.9331 (mt0) cc_final: 0.8795 (mp10) REVERT: S 17 GLU cc_start: 0.9379 (tp30) cc_final: 0.9138 (tp30) REVERT: W 165 MET cc_start: 0.9244 (mmt) cc_final: 0.8996 (mmm) REVERT: b 16 ASP cc_start: 0.9313 (m-30) cc_final: 0.8836 (t0) REVERT: b 318 MET cc_start: 0.8041 (mtm) cc_final: 0.7613 (mtp) REVERT: b 329 MET cc_start: 0.9332 (tpt) cc_final: 0.8925 (tpp) REVERT: f 26 ASN cc_start: 0.9290 (t0) cc_final: 0.9062 (t0) REVERT: m 64 SER cc_start: 0.8833 (t) cc_final: 0.8499 (p) REVERT: r 150 MET cc_start: 0.8360 (tmm) cc_final: 0.8113 (tmm) REVERT: v 90 MET cc_start: 0.7765 (mpp) cc_final: 0.7465 (mpp) REVERT: w 140 GLU cc_start: 0.9442 (mm-30) cc_final: 0.8899 (mm-30) REVERT: x 398 MET cc_start: 0.9230 (mpp) cc_final: 0.8737 (mpp) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 1.5748 time to fit residues: 825.9278 Evaluate side-chains 276 residues out of total 4454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 5.946 ------------------------------------------------------------------------------- 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: 0.9980 chunk 419 optimal weight: 6.9990 chunk 561 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 486 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 146 optimal weight: 30.0000 chunk 528 optimal weight: 7.9990 chunk 221 optimal weight: 6.9990 chunk 542 optimal weight: 9.9990 chunk 66 optimal weight: 50.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** 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** ** J 101 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 21 ASN ** 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 411 HIS ** r 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 24 ASN ** 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 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.050869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.040359 restraints weight = 3320629.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.041444 restraints weight = 1644850.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.042108 restraints weight = 1026865.615| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.6305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 80488 Z= 0.182 Angle : 0.533 7.799 116485 Z= 0.281 Chirality : 0.034 0.198 14366 Planarity : 0.004 0.064 8780 Dihedral : 24.436 178.711 30586 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.57 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -0.69 (0.12), residues: 5054 helix: 1.19 (0.13), residues: 1671 sheet: -1.15 (0.18), residues: 742 loop : -1.35 (0.12), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP x 322 HIS 0.006 0.001 HIS x 228 PHE 0.015 0.001 PHE B 209 TYR 0.017 0.001 TYR S 165 ARG 0.004 0.000 ARG M 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27361.55 seconds wall clock time: 475 minutes 9.24 seconds (28509.24 seconds total)