Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 15:36:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohu_12909/04_2023/7ohu_12909.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohu_12909/04_2023/7ohu_12909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohu_12909/04_2023/7ohu_12909.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohu_12909/04_2023/7ohu_12909.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohu_12909/04_2023/7ohu_12909.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohu_12909/04_2023/7ohu_12909.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1840 5.49 5 S 79 5.16 5 C 38832 2.51 5 N 13380 2.21 5 O 18746 1.98 5 H 54773 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B ASP 386": "OD1" <-> "OD2" Residue "C ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C ARG 326": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 104": "OE1" <-> "OE2" Residue "F GLU 24": "OE1" <-> "OE2" Residue "F ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 182": "OD1" <-> "OD2" Residue "F PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 158": "OD1" <-> "OD2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "G ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 228": "OE1" <-> "OE2" Residue "H TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 11": "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 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 111": "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 ARG 173": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 189": "OE1" <-> "OE2" Residue "L ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 107": "OE1" <-> "OE2" Residue "L PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 47": "OD1" <-> "OD2" Residue "M PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 8": "OE1" <-> "OE2" Residue "N ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ASP 124": "OD1" <-> "OD2" Residue "N ASP 145": "OD1" <-> "OD2" Residue "N TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 4": "OE1" <-> "OE2" Residue "O ASP 56": "OD1" <-> "OD2" Residue "O PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 151": "OD1" <-> "OD2" Residue "O PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 40": "OE1" <-> "OE2" Residue "P ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P GLU 147": "OE1" <-> "OE2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "Q PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 21": "OE1" <-> "OE2" Residue "S PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 104": "OE1" <-> "OE2" Residue "S ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ASP 27": "OD1" <-> "OD2" Residue "V ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W ARG 31": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 79": "OE1" <-> "OE2" Residue "W ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 83": "OE1" <-> "OE2" Residue "W PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 115": "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 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 193": "OE1" <-> "OE2" Residue "W ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ASP 224": "OD1" <-> "OD2" Residue "Y TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ASP 54": "OD1" <-> "OD2" Residue "Y GLU 55": "OE1" <-> "OE2" Residue "Y ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 80": "OD1" <-> "OD2" Residue "b ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 144": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 236": "OE1" <-> "OE2" Residue "b TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 325": "OE1" <-> "OE2" Residue "b GLU 326": "OE1" <-> "OE2" Residue "b ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 418": "OD1" <-> "OD2" Residue "b ASP 424": "OD1" <-> "OD2" Residue "b PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 459": "OE1" <-> "OE2" Residue "b GLU 461": "OE1" <-> "OE2" Residue "b GLU 466": "OE1" <-> "OE2" Residue "e ASP 23": "OD1" <-> "OD2" Residue "e TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f GLU 58": "OE1" <-> "OE2" Residue "f ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h GLU 15": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "h ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i GLU 66": "OE1" <-> "OE2" Residue "j PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "u TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "u ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u GLU 28": "OE1" <-> "OE2" Residue "u PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "u ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "u ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 80": "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 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "u ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "y TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "y ASP 44": "OD1" <-> "OD2" Residue "y ASP 78": "OD1" <-> "OD2" Residue "y ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "y ASP 122": "OD1" <-> "OD2" Residue "y GLU 124": "OE1" <-> "OE2" Residue "y PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "y TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "y ASP 209": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 127652 Number of models: 1 Model: "" Number of chains: 29 Chain: "1" Number of atoms: 54436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1692, 54436 Classifications: {'RNA': 1692} Modifications used: {'3*END': 1, 'rna2p_pur': 178, 'rna2p_pyr': 108, 'rna3p_pur': 772, 'rna3p_pyr': 634} Link IDs: {'rna2p': 286, 'rna3p': 1405} Chain breaks: 25 Chain: "2" Number of atoms: 4737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 4737 Classifications: {'RNA': 148} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 12, 'rna3p_pur': 62, 'rna3p_pyr': 61} Link IDs: {'rna2p': 24, 'rna3p': 123} Chain breaks: 2 Chain: "B" Number of atoms: 5336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5336 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain breaks: 2 Chain: "C" Number of atoms: 5260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5260 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 319} Chain breaks: 2 Chain: "E" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2376 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 137} Chain breaks: 1 Chain: "F" Number of atoms: 3700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3700 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain: "G" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2488 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 8, 'TRANS': 147} Chain breaks: 1 Chain: "H" Number of atoms: 3086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 3086 Classifications: {'peptide': 190} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "L" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1782 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2179 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "N" Number of atoms: 3079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3079 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "O" Number of atoms: 3215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3215 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1694 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain breaks: 2 Chain: "Q" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2101 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "S" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2904 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "V" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1890 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain breaks: 1 Chain: "W" Number of atoms: 3773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3773 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "Y" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2060 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "b" Number of atoms: 6718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6718 Classifications: {'peptide': 411} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 391} Chain breaks: 4 Chain: "e" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2090 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} 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: "h" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Chain: "i" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1236 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "j" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1137 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'TRANS': 69} Chain: "r" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1288 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "u" Number of atoms: 1987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1987 Classifications: {'peptide': 116} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} 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: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 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 A0FCZ SG CYS j 19 124.535 63.845 139.461 1.00109.48 S ATOM A0FEC SG CYS j 22 121.412 63.829 137.340 1.00 87.45 S ATOM A0FK1 SG CYS j 34 123.159 67.151 138.262 1.00 98.44 S ATOM A0FKY SG CYS j 37 121.253 65.191 140.882 1.00 75.92 S ATOM A0H9F SG CYS u 6 169.944 116.117 55.007 1.00170.73 S ATOM A0HAR SG CYS u 9 170.912 112.226 55.906 1.00221.58 S ATOM A0HKO SG CYS u 32 167.566 113.403 55.094 1.00299.18 S ATOM A0HMK SG CYS u 36 168.790 112.592 57.920 1.00197.00 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: 39.95, per 1000 atoms: 0.31 Number of scatterers: 127652 At special positions: 0 Unit cell: (224.399, 226.526, 235.034, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 79 16.00 P 1840 15.00 O 18746 8.00 N 13380 7.00 C 38832 6.00 H 54773 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: 79.25 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " 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 36 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 6 " Number of angles added : 12 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7922 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 45 sheets defined 42.9% alpha, 15.1% beta 563 base pairs and 815 stacking pairs defined. Time for finding SS restraints: 44.34 Creating SS restraints... Processing helix chain 'B' and resid 111 through 118 removed outlier: 3.796A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 141 through 155 removed outlier: 3.510A pdb=" N ILE B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 44 through 47 Processing helix chain 'C' and resid 114 through 129 removed outlier: 3.663A pdb=" N THR C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 173 through 179 removed outlier: 4.540A pdb=" N ASP C 177 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 196 removed outlier: 4.130A pdb=" N ASN C 196 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 220 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 252 through 263 removed outlier: 4.274A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 removed outlier: 3.612A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 299 removed outlier: 3.672A pdb=" N ALA C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.601A pdb=" N ARG C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 327 " --> pdb=" O VAL C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.214A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU C 337 " --> pdb=" O VAL C 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 131 through 151 removed outlier: 3.559A pdb=" N VAL E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'F' and resid 22 through 72 removed outlier: 4.430A pdb=" N ALA F 27 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ALA F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.513A pdb=" N VAL F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 130 removed outlier: 3.683A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.787A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 222 through 226 Processing helix chain 'F' and resid 235 through 244 Processing helix chain 'G' and resid 83 through 96 Processing helix chain 'G' and resid 101 through 116 removed outlier: 3.815A pdb=" N ALA G 115 " --> pdb=" O LYS G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 160 through 173 removed outlier: 4.379A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU G 166 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Proline residue: G 167 - end of helix Processing helix chain 'G' and resid 182 through 191 removed outlier: 4.061A pdb=" N LEU G 186 " --> pdb=" O GLY G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 222 removed outlier: 3.571A pdb=" N ALA G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 227 Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.759A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 Processing helix chain 'H' and resid 116 through 120 Processing helix chain 'H' and resid 150 through 164 Processing helix chain 'L' and resid 27 through 46 removed outlier: 3.646A pdb=" N LYS L 45 " --> pdb=" O THR L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 83 Processing helix chain 'L' and resid 86 through 93 removed outlier: 3.674A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE L 93 " --> pdb=" O TYR L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 96 Processing helix chain 'M' and resid 97 through 111 removed outlier: 3.671A pdb=" N ILE M 103 " --> pdb=" O TRP M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 135 Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.835A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.752A pdb=" N LEU N 22 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU N 29 " --> pdb=" O VAL N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 145 Processing helix chain 'N' and resid 148 through 157 removed outlier: 3.568A pdb=" N ILE N 151 " --> pdb=" O TYR N 148 " (cutoff:3.500A) Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 177 through 184 removed outlier: 5.206A pdb=" N ASN N 182 " --> pdb=" O LYS N 179 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS N 184 " --> pdb=" O ASN N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 195 Processing helix chain 'O' and resid 15 through 29 Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.753A pdb=" N LYS O 60 " --> pdb=" O ASP O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 87 removed outlier: 3.730A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 100 Processing helix chain 'O' and resid 111 through 115 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 162 removed outlier: 3.875A pdb=" N LYS O 159 " --> pdb=" O LYS O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 163 through 186 removed outlier: 3.542A pdb=" N TYR O 167 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 197 removed outlier: 3.603A pdb=" N ALA O 196 " --> pdb=" O LYS O 192 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.588A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR P 32 " --> pdb=" O ASN P 28 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'Q' and resid 23 through 40 Processing helix chain 'Q' and resid 42 through 54 removed outlier: 3.785A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 73 removed outlier: 3.639A pdb=" N GLN Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 117 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'S' and resid 33 through 49 Processing helix chain 'S' and resid 98 through 114 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 'V' and resid 66 through 70 removed outlier: 3.663A pdb=" N ARG V 70 " --> pdb=" O PRO V 67 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 126 Processing helix chain 'V' and resid 126 through 132 Processing helix chain 'W' and resid 19 through 37 removed outlier: 4.013A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL W 30 " --> pdb=" O ILE W 26 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG W 31 " --> pdb=" O PHE W 27 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 59 Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 88 through 94 removed outlier: 3.903A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS W 94 " --> pdb=" O TYR W 90 " (cutoff:3.500A) 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 'Y' and resid 11 through 21 Processing helix chain 'Y' and resid 23 through 31 removed outlier: 4.127A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 122 Processing helix chain 'b' and resid 13 through 29 Processing helix chain 'b' and resid 38 through 68 removed outlier: 3.565A pdb=" N LYS b 49 " --> pdb=" O PHE b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 74 removed outlier: 4.125A pdb=" N VAL b 74 " --> pdb=" O ILE b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 86 removed outlier: 3.564A pdb=" N ASP b 80 " --> pdb=" O PRO b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 118 removed outlier: 3.723A pdb=" N PHE b 118 " --> pdb=" O ARG b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 142 removed outlier: 3.825A pdb=" N MET b 136 " --> pdb=" O ALA b 132 " (cutoff:3.500A) Processing helix chain 'b' and resid 143 through 158 removed outlier: 3.508A pdb=" N TYR b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 188 removed outlier: 3.590A pdb=" N LEU b 184 " --> pdb=" O LYS b 180 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG b 185 " --> pdb=" O SER b 181 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR b 188 " --> pdb=" O LEU b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 233 through 246 removed outlier: 3.631A pdb=" N GLN b 238 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 275 removed outlier: 3.810A pdb=" N GLN b 267 " --> pdb=" O THR b 263 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER b 273 " --> pdb=" O LYS b 269 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE b 274 " --> pdb=" O LEU b 270 " (cutoff:3.500A) Processing helix chain 'b' and resid 278 through 282 removed outlier: 3.821A pdb=" N LYS b 281 " --> pdb=" O PHE b 278 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER b 282 " --> pdb=" O ALA b 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 278 through 282' Processing helix chain 'b' and resid 302 through 311 removed outlier: 4.055A pdb=" N VAL b 309 " --> pdb=" O LEU b 305 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 341 removed outlier: 3.572A pdb=" N VAL b 328 " --> pdb=" O LEU b 324 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS b 334 " --> pdb=" O GLU b 330 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 removed outlier: 4.054A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 406 removed outlier: 4.409A pdb=" N ALA b 404 " --> pdb=" O ARG b 400 " (cutoff:3.500A) Processing helix chain 'b' and resid 441 through 446 removed outlier: 3.808A pdb=" N PHE b 444 " --> pdb=" O VAL b 441 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU b 445 " --> pdb=" O TYR b 442 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP b 446 " --> pdb=" O ASP b 443 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 441 through 446' Processing helix chain 'b' and resid 448 through 453 Processing helix chain 'b' and resid 454 through 463 removed outlier: 4.297A pdb=" N GLU b 457 " --> pdb=" O GLN b 454 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLU b 458 " --> pdb=" O ALA b 455 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU b 459 " --> pdb=" O LEU b 456 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU b 460 " --> pdb=" O GLU b 457 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS b 462 " --> pdb=" O GLU b 459 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 60 through 64 Processing helix chain 'e' and resid 78 through 84 removed outlier: 3.676A pdb=" N THR e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 87 No H-bonds generated for 'chain 'e' and resid 85 through 87' Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.787A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (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 'h' and resid 5 through 10 Processing helix chain 'h' and resid 13 through 35 Processing helix chain 'h' and resid 42 through 70 removed outlier: 3.815A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL h 66 " --> pdb=" O GLN h 62 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 81 Processing helix chain 'h' and resid 85 through 91 Processing helix chain 'h' and resid 93 through 98 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 35 through 49 removed outlier: 3.562A pdb=" N ILE i 47 " --> pdb=" O LEU i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 64 Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 98 Processing helix chain 'j' and resid 50 through 58 Processing helix chain 'j' and resid 66 through 68 No H-bonds generated for 'chain 'j' and resid 66 through 68' Processing helix chain 'j' and resid 69 through 76 removed outlier: 3.686A pdb=" N ASN j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'r' and resid 7 through 12 removed outlier: 3.688A pdb=" N LYS r 12 " --> pdb=" O GLU r 8 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 41 removed outlier: 3.973A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER r 36 " --> pdb=" O SER r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 74 removed outlier: 3.552A pdb=" N GLN r 70 " --> pdb=" O LYS r 66 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 52 through 59 Processing helix chain 'u' and resid 66 through 71 removed outlier: 3.830A pdb=" N PHE u 71 " --> pdb=" O SER u 67 " (cutoff:3.500A) Processing helix chain 'u' and resid 82 through 104 Processing helix chain 'u' and resid 106 through 111 removed outlier: 3.612A pdb=" N ASN u 110 " --> pdb=" O ALA u 106 " (cutoff:3.500A) Processing helix chain 'y' and resid 32 through 43 removed outlier: 4.385A pdb=" N SER y 36 " --> pdb=" O GLU y 32 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA y 37 " --> pdb=" O ASN y 33 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE y 38 " --> pdb=" O PHE y 34 " (cutoff:3.500A) removed outlier: 3.671A 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 87 Processing helix chain 'y' and resid 103 through 107 Processing helix chain 'y' and resid 122 through 134 removed outlier: 3.722A pdb=" N GLU y 126 " --> pdb=" O ASP y 122 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU y 127 " --> pdb=" O ARG y 123 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU y 128 " --> pdb=" O GLU y 124 " (cutoff:3.500A) Processing helix chain 'y' and resid 141 through 145 Processing helix chain 'y' and resid 147 through 151 Processing helix chain 'y' and resid 166 through 178 removed outlier: 3.915A pdb=" N LEU y 176 " --> pdb=" O GLU y 172 " (cutoff:3.500A) Processing helix chain 'y' and resid 192 through 196 Processing helix chain 'y' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain 'B' and resid 274 through 275 removed outlier: 4.708A pdb=" N LYS B 281 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B 321 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL B 72 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL B 57 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU B 74 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR B 55 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 76 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N MET B 53 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP B 59 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU B 356 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 274 through 275 removed outlier: 4.943A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP B 59 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU B 356 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 106 removed outlier: 6.985A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 157 " --> pdb=" O TYR B 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 106 removed outlier: 6.985A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 15 through 21 removed outlier: 5.698A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL C 151 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU C 150 " --> pdb=" O TRP C 250 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR C 209 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 79 removed outlier: 6.471A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N THR E 89 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE E 41 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR E 87 " --> pdb=" O ILE E 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.403A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL F 134 " --> pdb=" O GLY F 230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 153 through 155 Processing sheet with id=AB1, first strand: chain 'G' and resid 133 through 134 removed outlier: 3.833A pdb=" N LEU G 200 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU G 150 " --> pdb=" O LEU G 200 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 5 through 11 Processing sheet with id=AB3, first strand: chain 'H' and resid 32 through 37 removed outlier: 3.501A pdb=" N LYS H 26 " --> pdb=" O SER H 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 133 through 136 removed outlier: 6.682A pdb=" N LYS H 89 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AB6, first strand: chain 'L' and resid 23 through 24 removed outlier: 6.393A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AB8, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AB9, first strand: chain 'M' and resid 14 through 15 removed outlier: 3.872A pdb=" N PHE S 150 " --> pdb=" O VAL M 15 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 53 through 59 removed outlier: 5.513A pdb=" N GLY M 48 " --> pdb=" O PRO M 54 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.287A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE N 130 " --> pdb=" O VAL N 64 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 6 through 10 Processing sheet with id=AC4, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AC5, first strand: chain 'P' and resid 14 through 22 removed outlier: 4.301A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR P 151 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL P 114 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Q' and resid 62 through 63 removed outlier: 3.606A pdb=" N VAL Q 81 " --> pdb=" O THR Q 100 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU Q 104 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLY Q 85 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N PHE Q 106 " --> pdb=" O GLY Q 85 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL Q 87 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Q' and resid 62 through 63 removed outlier: 4.674A pdb=" N VAL Q 84 " --> pdb=" O LEU Q 140 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'S' and resid 25 through 31 removed outlier: 7.365A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 88 through 96 removed outlier: 3.748A pdb=" N TYR S 81 " --> pdb=" O HIS S 88 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASN S 74 " --> pdb=" O GLU S 128 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU S 128 " --> pdb=" O ASN S 74 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY S 76 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL S 126 " --> pdb=" O GLY S 76 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 22 through 25 removed outlier: 6.967A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 85 through 86 removed outlier: 3.762A pdb=" N LEU V 93 " --> pdb=" O TRP V 85 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE V 92 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL u 22 " --> pdb=" O PHE V 92 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR V 94 " --> pdb=" O VAL u 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'W' and resid 64 through 65 removed outlier: 3.801A pdb=" N GLY W 101 " --> pdb=" O LEU W 43 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL W 42 " --> pdb=" O ALA W 219 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'W' and resid 121 through 123 Processing sheet with id=AD5, first strand: chain 'W' and resid 135 through 136 removed outlier: 7.426A pdb=" N PHE W 135 " --> pdb=" O VAL W 188 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'W' and resid 174 through 176 Processing sheet with id=AD7, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AD8, first strand: chain 'Y' and resid 79 through 82 removed outlier: 3.647A pdb=" N SER Y 72 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU Y 55 " --> pdb=" O THR Y 107 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 86 through 88 Processing sheet with id=AE1, first strand: chain 'b' and resid 205 through 211 removed outlier: 6.035A pdb=" N LEU b 170 " --> pdb=" O ILE b 219 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N TYR b 252 " --> pdb=" O VAL b 286 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ASN b 288 " --> pdb=" O TYR b 252 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET b 254 " --> pdb=" O ASN b 288 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'e' and resid 72 through 76 removed outlier: 6.055A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'f' and resid 8 through 18 removed outlier: 9.798A pdb=" N VAL f 9 " --> pdb=" O ILE f 32 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE f 32 " --> pdb=" O VAL f 9 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N GLY f 11 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ILE f 30 " --> pdb=" O GLY f 11 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N HIS f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N SER f 28 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 11.461A pdb=" N SER f 15 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ASN f 26 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN f 17 " --> pdb=" O ASN f 24 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AE5, first strand: chain 'y' and resid 3 through 4 Processing sheet with id=AE6, first strand: chain 'y' and resid 17 through 19 removed outlier: 7.035A pdb=" N CYS y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR y 51 " --> pdb=" O CYS y 24 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N VAL y 26 " --> pdb=" O THR y 51 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'y' and resid 64 through 66 removed outlier: 3.720A pdb=" N GLN y 95 " --> pdb=" O LEU y 70 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'y' and resid 108 through 110 Processing sheet with id=AE9, first strand: chain 'y' and resid 152 through 154 removed outlier: 3.554A pdb=" N VAL y 182 " --> pdb=" O GLY y 159 " (cutoff:3.500A) 1366 hydrogen bonds defined for protein. 3837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1399 hydrogen bonds 2246 hydrogen bond angles 0 basepair planarities 563 basepair parallelities 815 stacking parallelities Total time for adding SS restraints: 73.22 Time building geometry restraints manager: 84.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.25: 61872 1.25 - 1.67: 70901 1.67 - 2.09: 131 2.09 - 2.51: 2 2.51 - 2.93: 1 Bond restraints: 132907 Sorted by residual: bond pdb=" O3' A 11062 " pdb=" P A 11098 " ideal model delta sigma weight residual 1.607 2.929 -1.322 1.50e-02 4.44e+03 7.76e+03 bond pdb=" CD2 TYR b 469 " pdb=" CE2 TYR b 469 " ideal model delta sigma weight residual 1.382 2.375 -0.993 3.00e-02 1.11e+03 1.09e+03 bond pdb=" CD1 TYR b 469 " pdb=" CE1 TYR b 469 " ideal model delta sigma weight residual 1.382 2.327 -0.945 3.00e-02 1.11e+03 9.93e+02 bond pdb=" CE2 TYR b 469 " pdb=" CZ TYR b 469 " ideal model delta sigma weight residual 1.378 1.952 -0.574 2.40e-02 1.74e+03 5.72e+02 bond pdb=" CE1 TYR b 469 " pdb=" CZ TYR b 469 " ideal model delta sigma weight residual 1.378 1.911 -0.533 2.40e-02 1.74e+03 4.93e+02 ... (remaining 132902 not shown) Histogram of bond angle deviations from ideal: 40.63 - 62.28: 1 62.28 - 83.94: 1 83.94 - 105.60: 9176 105.60 - 127.26: 226059 127.26 - 148.91: 4134 Bond angle restraints: 239371 Sorted by residual: angle pdb=" O3' A 11062 " pdb=" P A 11098 " pdb=" OP1 A 11098 " ideal model delta sigma weight residual 108.00 40.63 67.37 3.00e+00 1.11e-01 5.04e+02 angle pdb=" O3' A 11062 " pdb=" P A 11098 " pdb=" O5' A 11098 " ideal model delta sigma weight residual 104.00 81.08 22.92 1.50e+00 4.44e-01 2.33e+02 angle pdb=" O ALA u 106 " pdb=" C ALA u 106 " pdb=" N PHE u 107 " ideal model delta sigma weight residual 121.95 105.35 16.60 1.17e+00 7.31e-01 2.01e+02 angle pdb=" O3' A 11062 " pdb=" P A 11098 " pdb=" OP2 A 11098 " ideal model delta sigma weight residual 108.00 148.91 -40.91 3.00e+00 1.11e-01 1.86e+02 angle pdb=" N ALA u 106 " pdb=" CA ALA u 106 " pdb=" CB ALA u 106 " ideal model delta sigma weight residual 110.63 87.13 23.50 1.94e+00 2.66e-01 1.47e+02 ... (remaining 239366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 50767 35.94 - 71.88: 1686 71.88 - 107.82: 204 107.82 - 143.76: 32 143.76 - 179.70: 37 Dihedral angle restraints: 52726 sinusoidal: 38681 harmonic: 14045 Sorted by residual: dihedral pdb=" C4' G 1 644 " pdb=" C3' G 1 644 " pdb=" C2' G 1 644 " pdb=" C1' G 1 644 " ideal model delta sinusoidal sigma weight residual -35.00 35.04 -70.04 1 8.00e+00 1.56e-02 9.88e+01 dihedral pdb=" C4' G 1 661 " pdb=" C3' G 1 661 " pdb=" C2' G 1 661 " pdb=" C1' G 1 661 " ideal model delta sinusoidal sigma weight residual -35.00 35.00 -70.00 1 8.00e+00 1.56e-02 9.87e+01 dihedral pdb=" C5' G 1 661 " pdb=" C4' G 1 661 " pdb=" C3' G 1 661 " pdb=" O3' G 1 661 " ideal model delta sinusoidal sigma weight residual 147.00 79.92 67.08 1 8.00e+00 1.56e-02 9.16e+01 ... (remaining 52723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 13651 0.069 - 0.139: 622 0.139 - 0.208: 13 0.208 - 0.277: 31 0.277 - 0.347: 3 Chirality restraints: 14320 Sorted by residual: chirality pdb=" C1' U 1 988 " pdb=" O4' U 1 988 " pdb=" C2' U 1 988 " pdb=" N1 U 1 988 " both_signs ideal model delta sigma weight residual False 2.47 2.12 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C3' G 1 644 " pdb=" C4' G 1 644 " pdb=" O3' G 1 644 " pdb=" C2' G 1 644 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C3' G 1 661 " pdb=" C4' G 1 661 " pdb=" O3' G 1 661 " pdb=" C2' G 1 661 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 14317 not shown) Planarity restraints: 13039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR b 469 " 0.016 2.00e-02 2.50e+03 3.95e-02 4.68e+01 pdb=" CG TYR b 469 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR b 469 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR b 469 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR b 469 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR b 469 " -0.095 2.00e-02 2.50e+03 pdb=" CZ TYR b 469 " 0.064 2.00e-02 2.50e+03 pdb=" OH TYR b 469 " 0.008 2.00e-02 2.50e+03 pdb=" HD1 TYR b 469 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 TYR b 469 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TYR b 469 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR b 469 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA u 106 " -0.025 2.00e-02 2.50e+03 4.57e-02 2.08e+01 pdb=" N PHE u 107 " 0.078 2.00e-02 2.50e+03 pdb=" CA PHE u 107 " -0.017 2.00e-02 2.50e+03 pdb=" H PHE u 107 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 1 988 " -0.032 2.00e-02 2.50e+03 2.48e-02 1.84e+01 pdb=" N1 U 1 988 " 0.051 2.00e-02 2.50e+03 pdb=" C2 U 1 988 " -0.004 2.00e-02 2.50e+03 pdb=" O2 U 1 988 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U 1 988 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U 1 988 " -0.051 2.00e-02 2.50e+03 pdb=" O4 U 1 988 " 0.030 2.00e-02 2.50e+03 pdb=" C5 U 1 988 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U 1 988 " 0.005 2.00e-02 2.50e+03 pdb=" H5 U 1 988 " -0.005 2.00e-02 2.50e+03 pdb=" H3 U 1 988 " -0.007 2.00e-02 2.50e+03 pdb=" H6 U 1 988 " 0.007 2.00e-02 2.50e+03 ... (remaining 13036 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 4254 2.14 - 2.75: 197790 2.75 - 3.37: 344616 3.37 - 3.98: 467596 3.98 - 4.60: 700949 Nonbonded interactions: 1715205 Sorted by model distance: nonbonded pdb=" O LYS Y 69 " pdb=" H ASP Y 83 " model vdw 1.520 1.850 nonbonded pdb=" OD1 ASN y 111 " pdb=" H VAL y 114 " model vdw 1.522 1.850 nonbonded pdb=" OP2 U 13105 " pdb=" H1 G 13128 " model vdw 1.572 1.850 nonbonded pdb=" OP1 A 2 72 " pdb=" H ARG Y 52 " model vdw 1.575 1.850 nonbonded pdb=" OP2 U 1 210 " pdb=" H THR C 162 " model vdw 1.592 1.850 ... (remaining 1715200 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: 4.350 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: 1.160 Extract box with map and model: 20.760 Check model and map are aligned: 1.350 Set scattering table: 0.810 Process input model: 380.010 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.270 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 412.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 : 0.008 1.322 78134 Z= 0.544 Angle : 0.533 67.373 114440 Z= 0.268 Chirality : 0.033 0.347 14320 Planarity : 0.002 0.048 7650 Dihedral : 16.123 179.700 35106 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.01 (0.14), residues: 4122 helix: 1.89 (0.14), residues: 1562 sheet: 0.22 (0.23), residues: 542 loop : -0.12 (0.14), residues: 2018 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 698 time to evaluate : 5.390 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 outliers start: 16 outliers final: 8 residues processed: 710 average time/residue: 1.7471 time to fit residues: 1973.6457 Evaluate side-chains 460 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 452 time to evaluate : 5.352 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 1.6874 time to fit residues: 27.4199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 500 optimal weight: 20.0000 chunk 449 optimal weight: 5.9990 chunk 249 optimal weight: 0.1980 chunk 153 optimal weight: 9.9990 chunk 303 optimal weight: 8.9990 chunk 240 optimal weight: 8.9990 chunk 464 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 282 optimal weight: 6.9990 chunk 345 optimal weight: 8.9990 chunk 538 optimal weight: 9.9990 overall best weight: 6.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 104 GLN F 112 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS F 225 GLN ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 ASN P 96 GLN P 97 ASN Q 58 ASN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 217 GLN e 21 HIS h 20 GLN h 59 ASN h 99 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.995 78134 Z= 0.533 Angle : 0.612 23.641 114440 Z= 0.327 Chirality : 0.037 0.511 14320 Planarity : 0.005 0.060 7650 Dihedral : 15.851 178.317 26648 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.03 (0.13), residues: 4122 helix: 0.71 (0.12), residues: 1588 sheet: -0.27 (0.22), residues: 553 loop : -0.45 (0.14), residues: 1981 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 461 time to evaluate : 5.353 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 outliers start: 57 outliers final: 37 residues processed: 501 average time/residue: 1.4649 time to fit residues: 1174.1187 Evaluate side-chains 420 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 383 time to evaluate : 5.091 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 3 residues processed: 37 average time/residue: 1.0271 time to fit residues: 72.9510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 299 optimal weight: 10.0000 chunk 167 optimal weight: 30.0000 chunk 448 optimal weight: 4.9990 chunk 366 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 539 optimal weight: 20.0000 chunk 582 optimal weight: 0.0980 chunk 480 optimal weight: 10.0000 chunk 534 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 432 optimal weight: 20.0000 overall best weight: 5.6192 ------------------------------------------------------------------------------- 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 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN N 156 HIS ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 54 GLN ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 259 GLN r 10 HIS r 13 GLN r 14 HIS y 83 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.997 78134 Z= 0.498 Angle : 0.532 23.578 114440 Z= 0.286 Chirality : 0.034 0.284 14320 Planarity : 0.004 0.063 7650 Dihedral : 15.986 178.802 26648 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.17 % Favored : 94.81 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.06 (0.13), residues: 4122 helix: 0.78 (0.13), residues: 1591 sheet: -0.41 (0.21), residues: 560 loop : -0.52 (0.14), residues: 1971 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 397 time to evaluate : 4.841 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 outliers start: 33 outliers final: 17 residues processed: 421 average time/residue: 1.5074 time to fit residues: 1020.6005 Evaluate side-chains 387 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 370 time to evaluate : 5.379 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 3 residues processed: 17 average time/residue: 1.0966 time to fit residues: 39.8075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 533 optimal weight: 10.0000 chunk 405 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 362 optimal weight: 4.9990 chunk 541 optimal weight: 8.9990 chunk 573 optimal weight: 20.0000 chunk 282 optimal weight: 0.8980 chunk 513 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN M 119 GLN ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 182 ASN P 101 ASN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 99 GLN r 10 HIS ** y 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.003 78134 Z= 0.498 Angle : 0.542 23.568 114440 Z= 0.292 Chirality : 0.034 0.281 14320 Planarity : 0.004 0.065 7650 Dihedral : 16.147 179.191 26648 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.94 % Favored : 94.01 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.19 (0.13), residues: 4122 helix: 0.76 (0.13), residues: 1594 sheet: -0.51 (0.21), residues: 544 loop : -0.67 (0.14), residues: 1984 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 384 time to evaluate : 4.798 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 outliers start: 36 outliers final: 24 residues processed: 412 average time/residue: 1.6309 time to fit residues: 1089.6118 Evaluate side-chains 387 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 363 time to evaluate : 5.335 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 4 residues processed: 24 average time/residue: 1.1874 time to fit residues: 58.7581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 477 optimal weight: 10.0000 chunk 325 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 426 optimal weight: 30.0000 chunk 236 optimal weight: 1.9990 chunk 489 optimal weight: 20.0000 chunk 396 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 292 optimal weight: 7.9990 chunk 514 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 260 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 4 GLN ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 115 ASN ** y 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.998 78134 Z= 0.524 Angle : 0.579 23.560 114440 Z= 0.309 Chirality : 0.035 0.285 14320 Planarity : 0.004 0.069 7650 Dihedral : 16.432 179.560 26648 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.77 % Favored : 93.18 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.51 (0.13), residues: 4122 helix: 0.52 (0.13), residues: 1618 sheet: -0.68 (0.22), residues: 545 loop : -0.90 (0.14), residues: 1959 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 376 time to evaluate : 5.348 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 outliers start: 35 outliers final: 19 residues processed: 401 average time/residue: 1.5288 time to fit residues: 981.5454 Evaluate side-chains 377 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 358 time to evaluate : 5.767 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 4 residues processed: 19 average time/residue: 1.3585 time to fit residues: 49.0414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 192 optimal weight: 10.0000 chunk 516 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 336 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 573 optimal weight: 1.9990 chunk 476 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 189 optimal weight: 20.0000 chunk 301 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 121 ASN C 213 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 13 GLN ** r 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.007 78134 Z= 0.519 Angle : 0.569 23.520 114440 Z= 0.304 Chirality : 0.035 0.280 14320 Planarity : 0.004 0.070 7650 Dihedral : 16.538 179.456 26648 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.84 % Favored : 93.11 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.53 (0.13), residues: 4122 helix: 0.57 (0.13), residues: 1616 sheet: -0.78 (0.21), residues: 563 loop : -0.95 (0.14), residues: 1943 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 365 time to evaluate : 5.306 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 outliers start: 34 outliers final: 24 residues processed: 384 average time/residue: 1.5259 time to fit residues: 942.2284 Evaluate side-chains 371 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 347 time to evaluate : 5.350 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 4 residues processed: 24 average time/residue: 1.1313 time to fit residues: 54.6478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 553 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 326 optimal weight: 6.9990 chunk 418 optimal weight: 9.9990 chunk 324 optimal weight: 10.0000 chunk 482 optimal weight: 8.9990 chunk 320 optimal weight: 7.9990 chunk 571 optimal weight: 8.9990 chunk 357 optimal weight: 20.0000 chunk 348 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 70 GLN ** y 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.996 78134 Z= 0.560 Angle : 0.628 23.559 114440 Z= 0.334 Chirality : 0.037 0.435 14320 Planarity : 0.005 0.115 7650 Dihedral : 16.847 179.670 26648 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.64 % Favored : 92.31 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.95 (0.13), residues: 4122 helix: 0.20 (0.12), residues: 1611 sheet: -0.95 (0.22), residues: 555 loop : -1.18 (0.14), residues: 1956 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 342 time to evaluate : 4.844 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 outliers start: 36 outliers final: 24 residues processed: 366 average time/residue: 1.6318 time to fit residues: 972.4578 Evaluate side-chains 353 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 329 time to evaluate : 5.339 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 4 residues processed: 24 average time/residue: 1.2214 time to fit residues: 59.4438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 353 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 341 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 363 optimal weight: 8.9990 chunk 389 optimal weight: 6.9990 chunk 282 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 449 optimal weight: 9.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 GLN S 46 GLN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.013 78134 Z= 0.511 Angle : 0.575 23.457 114440 Z= 0.307 Chirality : 0.036 0.276 14320 Planarity : 0.004 0.074 7650 Dihedral : 16.850 179.567 26648 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.18 % Favored : 92.77 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4122 helix: 0.43 (0.13), residues: 1607 sheet: -0.96 (0.21), residues: 564 loop : -1.09 (0.14), residues: 1951 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 348 time to evaluate : 5.354 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 outliers start: 18 outliers final: 11 residues processed: 358 average time/residue: 1.5281 time to fit residues: 882.8284 Evaluate side-chains 349 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 338 time to evaluate : 5.373 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 11 average time/residue: 1.1972 time to fit residues: 28.8740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 519 optimal weight: 10.0000 chunk 547 optimal weight: 9.9990 chunk 499 optimal weight: 5.9990 chunk 532 optimal weight: 10.0000 chunk 320 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 chunk 418 optimal weight: 20.0000 chunk 163 optimal weight: 30.0000 chunk 481 optimal weight: 10.0000 chunk 503 optimal weight: 9.9990 chunk 530 optimal weight: 8.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.002 78134 Z= 0.575 Angle : 0.637 23.473 114440 Z= 0.339 Chirality : 0.038 0.285 14320 Planarity : 0.005 0.073 7650 Dihedral : 17.071 179.723 26648 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.47 % Favored : 91.48 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.13), residues: 4122 helix: 0.15 (0.13), residues: 1605 sheet: -1.08 (0.21), residues: 563 loop : -1.28 (0.14), residues: 1954 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 332 time to evaluate : 5.345 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 outliers start: 16 outliers final: 14 residues processed: 341 average time/residue: 1.5903 time to fit residues: 884.9063 Evaluate side-chains 338 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 324 time to evaluate : 4.775 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 14 average time/residue: 1.2760 time to fit residues: 35.7165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 349 optimal weight: 8.9990 chunk 563 optimal weight: 10.0000 chunk 343 optimal weight: 9.9990 chunk 267 optimal weight: 8.9990 chunk 391 optimal weight: 6.9990 chunk 590 optimal weight: 20.0000 chunk 543 optimal weight: 4.9990 chunk 470 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 363 optimal weight: 0.7980 chunk 288 optimal weight: 4.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.014 78134 Z= 0.495 Angle : 0.574 23.454 114440 Z= 0.306 Chirality : 0.035 0.277 14320 Planarity : 0.004 0.073 7650 Dihedral : 17.004 179.451 26648 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.94 % Favored : 93.01 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.78 (0.13), residues: 4122 helix: 0.47 (0.13), residues: 1605 sheet: -1.04 (0.21), residues: 567 loop : -1.15 (0.14), residues: 1950 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 350 time to evaluate : 5.404 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 outliers start: 8 outliers final: 7 residues processed: 354 average time/residue: 1.6078 time to fit residues: 932.6853 Evaluate side-chains 347 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 340 time to evaluate : 5.360 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 7 average time/residue: 1.3805 time to fit residues: 22.4258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 373 optimal weight: 0.9990 chunk 501 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 433 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 471 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 483 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 232 ASN ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.055076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.041917 restraints weight = 1584333.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.043076 restraints weight = 612891.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.043690 restraints weight = 384673.682| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.008 78134 Z= 0.482 Angle : 0.553 23.462 114440 Z= 0.295 Chirality : 0.034 0.279 14320 Planarity : 0.004 0.066 7650 Dihedral : 16.878 179.611 26648 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.30 % Favored : 92.65 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.57 (0.13), residues: 4122 helix: 0.71 (0.13), residues: 1606 sheet: -0.97 (0.22), residues: 566 loop : -1.08 (0.14), residues: 1950 =============================================================================== Job complete usr+sys time: 27596.70 seconds wall clock time: 478 minutes 44.67 seconds (28724.67 seconds total)