Starting phenix.real_space_refine on Fri Mar 15 00:47:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohy_12913/03_2024/7ohy_12913.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohy_12913/03_2024/7ohy_12913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohy_12913/03_2024/7ohy_12913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohy_12913/03_2024/7ohy_12913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohy_12913/03_2024/7ohy_12913.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohy_12913/03_2024/7ohy_12913.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 1837 5.49 5 S 80 5.16 5 C 38115 2.51 5 N 13139 2.21 5 O 18537 1.98 5 H 53608 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 36": "OD1" <-> "OD2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B ASP 140": "OD1" <-> "OD2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 211": "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 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 29": "OE1" <-> "OE2" Residue "F ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F GLU 54": "OE1" <-> "OE2" Residue "F GLU 78": "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 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G GLU 107": "OE1" <-> "OE2" Residue "G ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 112": "OE1" <-> "OE2" Residue "G TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 130": "OD1" <-> "OD2" 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 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 PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 118": "OE1" <-> "OE2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 40": "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 9": "OE1" <-> "OE2" Residue "N ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 29": "OE1" <-> "OE2" Residue "N PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N ASP 145": "OD1" <-> "OD2" Residue "N TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 40": "OE1" <-> "OE2" Residue "O PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 57": "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 PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 108": "OD1" <-> "OD2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "Q TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ASP 89": "OD1" <-> "OD2" Residue "Q ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 17": "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 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S GLU 130": "OE1" <-> "OE2" Residue "S TYR 139": "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 GLU 108": "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 ASP 47": "OD1" <-> "OD2" 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 TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 153": "OE1" <-> "OE2" Residue "W ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ASP 183": "OD1" <-> "OD2" 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 GLU 212": "OE1" <-> "OE2" Residue "W ASP 224": "OD1" <-> "OD2" Residue "W GLU 229": "OE1" <-> "OE2" Residue "Y TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y GLU 38": "OE1" <-> "OE2" 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 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 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ASP 80": "OD1" <-> "OD2" Residue "b TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 144": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ASP 164": "OD1" <-> "OD2" Residue "b TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 220": "OD1" <-> "OD2" 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 PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 301": "OE1" <-> "OE2" Residue "b ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 307": "OE1" <-> "OE2" Residue "b GLU 325": "OE1" <-> "OE2" Residue "b ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 380": "OE1" <-> "OE2" Residue "b PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 426": "OE1" <-> "OE2" Residue "b TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 460": "OE1" <-> "OE2" Residue "b GLU 466": "OE1" <-> "OE2" Residue "b TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e ASP 23": "OD1" <-> "OD2" Residue "e TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "e GLU 95": "OE1" <-> "OE2" Residue "f TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f GLU 33": "OE1" <-> "OE2" Residue "f TYR 44": "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 GLU 102": "OE1" <-> "OE2" Residue "h ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r ASP 19": "OD1" <-> "OD2" Residue "r ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r GLU 37": "OE1" <-> "OE2" Residue "u ARG 2": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "u TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "u ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "u ARG 75": "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 ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "y GLU 12": "OE1" <-> "OE2" Residue "y TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "y TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "y ARG 85": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "y ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "y GLU 124": "OE1" <-> "OE2" Residue "y TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "y GLU 171": "OE1" <-> "OE2" Residue "y TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 125318 Number of models: 1 Model: "" Number of chains: 28 Chain: "1" Number of atoms: 54311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1689, 54311 Classifications: {'RNA': 1689} Modifications used: {'3*END': 1, 'rna2p_pur': 166, 'rna2p_pyr': 115, 'rna3p_pur': 773, 'rna3p_pyr': 635} Link IDs: {'rna2p': 281, 'rna3p': 1407} Chain breaks: 22 Chain: "2" Number of atoms: 4733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 4733 Classifications: {'RNA': 148} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 14, 'rna3p_pur': 61, 'rna3p_pyr': 60} Link IDs: {'rna2p': 27, 'rna3p': 120} Chain breaks: 2 Chain: "B" Number of atoms: 5374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5374 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 5336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5336 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 326} Chain: "E" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 2497 Classifications: {'peptide': 151} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143} Chain breaks: 1 Chain: "F" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain: "G" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1751 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} 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: 1998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1998 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} 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: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1693 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain breaks: 1 Chain: "W" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3683 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 9, 'TRANS': 217} Chain breaks: 1 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: 6144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 6144 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 358} Chain breaks: 6 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: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2048 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} 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: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1250 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} 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 A0DL7 SG CYS j 19 128.046 63.914 135.460 1.00109.48 S ATOM A0DMK SG CYS j 22 124.922 63.927 133.316 1.00 87.45 S ATOM A0DS9 SG CYS j 34 126.405 67.230 134.630 1.00 98.44 S ATOM A0DT6 SG CYS j 37 124.689 64.794 136.997 1.00 75.92 S ATOM A0FGL SG CYS u 6 169.012 117.138 52.883 1.00170.73 S ATOM A0FHX SG CYS u 9 169.877 113.410 53.351 1.00221.58 S ATOM A0FRU SG CYS u 32 166.015 114.610 52.432 1.00299.18 S ATOM A0FTQ SG CYS u 36 167.217 113.269 55.165 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: 38.36, per 1000 atoms: 0.31 Number of scatterers: 125318 At special positions: 0 Unit cell: (225.462, 227.589, 222.272, 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 80 16.00 P 1837 15.00 O 18537 8.00 N 13139 7.00 C 38115 6.00 H 53608 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: 78.74 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " pdb=" ZN u 201 " 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 9 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 6 " Number of angles added : 12 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7658 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 48 sheets defined 43.2% alpha, 16.0% beta 547 base pairs and 821 stacking pairs defined. Time for finding SS restraints: 43.53 Creating SS restraints... Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 132 through 138 removed outlier: 4.106A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.639A pdb=" N SER B 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 381 removed outlier: 3.680A pdb=" N LYS B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS B 377 " --> pdb=" O PRO B 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 28 Processing helix chain 'C' and resid 31 through 44 removed outlier: 3.835A pdb=" N LYS C 44 " --> pdb=" O THR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 129 removed outlier: 3.635A pdb=" N THR C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 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 174 through 181 Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 214 through 221 removed outlier: 4.356A pdb=" N ASN C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) 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: 3.959A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 removed outlier: 3.793A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 299 Processing helix chain 'C' and resid 320 through 327 Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 339 through 342 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 150 removed outlier: 3.996A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'F' and resid 19 through 25 Processing helix chain 'F' and resid 25 through 73 removed outlier: 4.101A pdb=" N GLU F 29 " --> pdb=" O GLN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.506A pdb=" N VAL F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 130 Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.735A 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 234 through 244 removed outlier: 4.299A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 95 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 160 through 174 removed outlier: 4.209A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 4.814A 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 Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.707A pdb=" N VAL H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.683A pdb=" N ALA H 109 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 120 Processing helix chain 'H' and resid 150 through 165 removed outlier: 3.916A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 62 through 66 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 93 Processing helix chain 'L' and resid 106 through 123 Processing helix chain 'M' and resid 48 through 52 removed outlier: 3.722A pdb=" N GLY M 52 " --> pdb=" O PRO M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 97 removed outlier: 3.641A pdb=" N LYS M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 112 Processing helix chain 'M' and resid 113 through 135 Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.539A pdb=" N LEU N 7 " --> pdb=" O ALA N 3 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 32 removed outlier: 3.575A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 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 Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 177 through 184 removed outlier: 5.201A pdb=" N ASN N 182 " --> pdb=" O LYS N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 196 Processing helix chain 'O' and resid 15 through 30 Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 46 through 59 removed outlier: 3.635A pdb=" N PHE O 57 " --> pdb=" O LYS O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 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 146 Processing helix chain 'O' and resid 149 through 186 removed outlier: 4.616A pdb=" N SER O 163 " --> pdb=" O LYS O 159 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLU O 166 " --> pdb=" O VAL O 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 198 Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 41 through 53 Processing helix chain 'P' and resid 70 through 75 Processing helix chain 'P' and resid 85 through 106 Processing helix chain 'Q' and resid 23 through 41 Processing helix chain 'Q' and resid 42 through 53 removed outlier: 3.622A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 72 Processing helix chain 'Q' and resid 75 through 79 removed outlier: 3.745A pdb=" N ASN Q 78 " --> pdb=" O GLY Q 75 " (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 removed outlier: 3.771A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 56 Processing helix chain 'S' and resid 98 through 113 Processing helix chain 'S' and resid 117 through 119 No H-bonds generated for 'chain 'S' and resid 117 through 119' Processing helix chain 'S' and resid 137 through 143 removed outlier: 4.015A pdb=" N PHE S 143 " --> pdb=" O TYR S 139 " (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 18 through 35 removed outlier: 3.823A pdb=" N ASN W 22 " --> pdb=" O LYS W 18 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 60 removed outlier: 4.179A pdb=" N TRP W 60 " --> pdb=" O ILE W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 80 through 84 Processing helix chain 'W' and resid 89 through 96 removed outlier: 3.812A pdb=" N SER W 93 " --> pdb=" O LEU W 89 " (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 167 Processing helix chain 'W' and resid 196 through 207 Processing helix chain 'Y' and resid 11 through 22 Processing helix chain 'Y' and resid 23 through 31 removed outlier: 3.782A 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 123 Processing helix chain 'b' and resid 13 through 28 Processing helix chain 'b' and resid 39 through 68 removed outlier: 3.622A pdb=" N THR b 53 " --> pdb=" O LYS b 49 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY b 54 " --> pdb=" O VAL b 50 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU b 55 " --> pdb=" O LYS b 51 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY b 56 " --> pdb=" O TYR b 52 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE b 57 " --> pdb=" O THR b 53 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 75 removed outlier: 3.551A pdb=" N VAL b 74 " --> pdb=" O ASN b 70 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N HIS b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 70 through 75' Processing helix chain 'b' and resid 75 through 86 Processing helix chain 'b' and resid 87 through 105 removed outlier: 3.969A pdb=" N VAL b 105 " --> pdb=" O ALA b 101 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 143 Processing helix chain 'b' and resid 143 through 158 removed outlier: 3.750A pdb=" N HIS b 156 " --> pdb=" O GLN b 152 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 188 Processing helix chain 'b' and resid 233 through 246 removed outlier: 3.554A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 275 Processing helix chain 'b' and resid 276 through 278 No H-bonds generated for 'chain 'b' and resid 276 through 278' Processing helix chain 'b' and resid 302 through 308 Processing helix chain 'b' and resid 309 through 312 removed outlier: 3.601A pdb=" N VAL b 312 " --> pdb=" O VAL b 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 309 through 312' Processing helix chain 'b' and resid 325 through 342 removed outlier: 3.653A pdb=" N LEU b 339 " --> pdb=" O ALA b 335 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU b 340 " --> pdb=" O CYS b 336 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 removed outlier: 4.393A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN b 384 " --> pdb=" O GLU b 380 " (cutoff:3.500A) Processing helix chain 'b' and resid 442 through 445 removed outlier: 3.695A pdb=" N LEU b 445 " --> pdb=" O TYR b 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 442 through 445' Processing helix chain 'b' and resid 449 through 455 removed outlier: 4.001A pdb=" N ALA b 455 " --> pdb=" O ALA b 451 " (cutoff:3.500A) Processing helix chain 'b' and resid 455 through 466 removed outlier: 4.325A pdb=" N GLU b 461 " --> pdb=" O GLU b 457 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU b 464 " --> pdb=" O GLU b 460 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.795A 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 36 through 38 No H-bonds generated for 'chain 'h' and resid 36 through 38' Processing helix chain 'h' and resid 41 through 70 removed outlier: 3.777A pdb=" N LYS h 45 " --> pdb=" O LEU h 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 90 Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'j' and resid 50 through 58 Processing helix chain 'j' and resid 67 through 77 removed outlier: 4.394A pdb=" N SER j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 19 through 41 removed outlier: 4.005A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER r 36 " --> pdb=" O SER r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 71 Processing helix chain 'u' and resid 33 through 43 Processing helix chain 'u' and resid 45 through 49 Processing helix chain 'u' and resid 52 through 59 Processing helix chain 'u' and resid 66 through 71 removed outlier: 3.509A pdb=" N PHE u 71 " --> pdb=" O SER u 67 " (cutoff:3.500A) Processing helix chain 'u' and resid 82 through 112 removed outlier: 4.071A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG u 95 " --> pdb=" O LYS u 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG u 105 " --> pdb=" O GLN u 101 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 16 Processing helix chain 'y' and resid 31 through 42 removed outlier: 4.259A pdb=" N TYR y 35 " --> pdb=" O SER y 31 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE y 38 " --> pdb=" O PHE y 34 " (cutoff:3.500A) Processing helix chain 'y' and resid 43 through 46 removed outlier: 3.770A pdb=" N ILE y 46 " --> pdb=" O GLY y 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 43 through 46' Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 107 Processing helix chain 'y' and resid 122 through 134 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 Processing helix chain 'y' and resid 192 through 197 Processing helix chain 'y' and resid 211 through 223 Processing sheet with id=AA1, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.726A pdb=" N LEU B 356 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP B 59 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE B 215 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS B 281 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE B 321 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 324 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 77 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG B 70 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY B 52 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASP B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LYS B 50 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 98 through 106 removed outlier: 6.791A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 106 removed outlier: 6.791A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.676A pdb=" N VAL C 151 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU C 150 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 62 through 63 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: 3.521A pdb=" N LYS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE E 85 " --> pdb=" O ILE E 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.509A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 7.589A 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 177 through 180 removed outlier: 6.459A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (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: 3.823A pdb=" N ILE M 6 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE H 20 " --> pdb=" O ILE M 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 133 through 136 removed outlier: 6.128A pdb=" N ARG H 91 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL H 181 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL H 93 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE H 179 " --> pdb=" O VAL H 93 " (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: 6.566A 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 124 through 125 removed outlier: 3.604A pdb=" N ALA h 117 " --> pdb=" O ILE L 124 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 56 through 59 removed outlier: 8.054A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.268A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 6 through 10 removed outlier: 6.257A pdb=" N VAL O 7 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL O 36 " --> pdb=" O VAL O 7 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE O 9 " --> pdb=" O VAL O 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AC4, first strand: chain 'P' and resid 14 through 22 removed outlier: 4.214A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS P 145 " --> pdb=" O VAL P 119 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL P 119 " --> pdb=" O HIS P 145 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU P 147 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE P 117 " --> pdb=" O GLU P 147 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL P 149 " --> pdb=" O SER P 115 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP P 39 " --> pdb=" O VAL P 114 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AC6, first strand: chain 'Q' and resid 62 through 63 removed outlier: 3.897A pdb=" N LEU Q 104 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLY Q 85 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE Q 106 " --> pdb=" O GLY Q 85 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL Q 87 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA Q 103 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AC8, first strand: chain 'S' and resid 25 through 31 Processing sheet with id=AC9, first strand: chain 'S' and resid 87 through 96 removed outlier: 3.528A pdb=" N LYS S 125 " --> pdb=" O TRP S 78 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ASP S 82 " --> pdb=" O ILE S 121 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE S 121 " --> pdb=" O ASP S 82 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 22 through 25 removed outlier: 6.670A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 8.086A 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 87 removed outlier: 3.692A pdb=" N VAL V 91 " --> pdb=" O ARG V 87 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE V 92 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL u 22 " --> pdb=" O PHE V 92 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TYR V 94 " --> pdb=" O VAL u 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'V' and resid 114 through 118 removed outlier: 8.015A pdb=" N ILE V 114 " --> pdb=" O GLY V 134 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL V 136 " --> pdb=" O ILE V 114 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N GLY V 116 " --> pdb=" O VAL V 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'W' and resid 64 through 66 removed outlier: 6.604A pdb=" N VAL W 40 " --> pdb=" O TYR W 220 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR W 220 " --> pdb=" O VAL W 40 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL W 42 " --> pdb=" O SER W 218 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'W' and resid 121 through 123 Processing sheet with id=AD6, first strand: chain 'W' and resid 136 through 137 Processing sheet with id=AD7, first strand: chain 'W' and resid 174 through 176 Processing sheet with id=AD8, first strand: chain 'Y' and resid 33 through 34 Processing sheet with id=AD9, first strand: chain 'Y' and resid 79 through 82 removed outlier: 3.743A pdb=" N SER Y 72 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY Y 68 " --> pdb=" O VAL Y 56 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL Y 56 " --> pdb=" O GLY Y 68 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLU Y 55 " --> pdb=" O THR Y 107 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 86 through 88 Processing sheet with id=AE2, first strand: chain 'b' and resid 205 through 211 removed outlier: 3.906A pdb=" N TYR b 205 " --> pdb=" O ASP b 220 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG b 168 " --> pdb=" O ARG b 215 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'b' and resid 435 through 436 Processing sheet with id=AE4, first strand: chain 'e' and resid 72 through 76 removed outlier: 6.032A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'f' and resid 8 through 18 removed outlier: 9.990A pdb=" N VAL f 9 " --> pdb=" O ILE f 32 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE f 32 " --> pdb=" O VAL f 9 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLY f 11 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ILE f 30 " --> pdb=" O GLY f 11 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N HIS f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 9.824A pdb=" N SER f 28 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 11.336A pdb=" N SER f 15 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ASN f 26 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN f 17 " --> pdb=" O ASN f 24 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'j' and resid 16 through 17 removed outlier: 3.577A pdb=" N THR j 33 " --> pdb=" O HIS j 28 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'u' and resid 4 through 5 Processing sheet with id=AE8, first strand: chain 'y' and resid 2 through 5 Processing sheet with id=AE9, first strand: chain 'y' and resid 17 through 19 removed outlier: 6.702A pdb=" N CYS y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'y' and resid 69 through 72 removed outlier: 6.118A pdb=" N LEU y 70 " --> pdb=" O GLN y 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'y' and resid 108 through 110 Processing sheet with id=AF3, first strand: chain 'y' and resid 152 through 154 removed outlier: 6.424A pdb=" N GLY y 159 " --> pdb=" O VAL y 182 " (cutoff:3.500A) 1377 hydrogen bonds defined for protein. 3843 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1361 hydrogen bonds 2196 hydrogen bond angles 0 basepair planarities 547 basepair parallelities 821 stacking parallelities Total time for adding SS restraints: 63.98 Time building geometry restraints manager: 83.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 53576 1.03 - 1.23: 489 1.23 - 1.42: 36431 1.42 - 1.62: 39921 1.62 - 1.81: 128 Bond restraints: 130545 Sorted by residual: bond pdb=" N GLY N 2 " pdb=" CA GLY N 2 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.45e+00 bond pdb=" N GLY B 12 " pdb=" CA GLY B 12 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.15e+00 bond pdb=" N SER j 15 " pdb=" CA SER j 15 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" N ARG W 3 " pdb=" CA ARG W 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N HIS Q 15 " pdb=" CA HIS Q 15 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 ... (remaining 130540 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.20: 11912 107.20 - 113.97: 143281 113.97 - 120.74: 48171 120.74 - 127.51: 28117 127.51 - 134.28: 3626 Bond angle restraints: 235107 Sorted by residual: angle pdb=" C2' U 1 471 " pdb=" C1' U 1 471 " pdb=" N1 U 1 471 " ideal model delta sigma weight residual 112.00 117.50 -5.50 1.50e+00 4.44e-01 1.35e+01 angle pdb=" C4' G 13369 " pdb=" C3' G 13369 " pdb=" O3' G 13369 " ideal model delta sigma weight residual 109.40 114.80 -5.40 1.50e+00 4.44e-01 1.29e+01 angle pdb=" OP1 G 1 781 " pdb=" P G 1 781 " pdb=" OP2 G 1 781 " ideal model delta sigma weight residual 119.60 109.30 10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" OP1 C 1 166 " pdb=" P C 1 166 " pdb=" OP2 C 1 166 " ideal model delta sigma weight residual 119.60 109.37 10.23 3.00e+00 1.11e-01 1.16e+01 angle pdb=" OP1 G 2 114 " pdb=" P G 2 114 " pdb=" OP2 G 2 114 " ideal model delta sigma weight residual 119.60 109.38 10.22 3.00e+00 1.11e-01 1.16e+01 ... (remaining 235102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 57325 35.93 - 71.85: 5389 71.85 - 107.78: 574 107.78 - 143.71: 34 143.71 - 179.63: 38 Dihedral angle restraints: 63360 sinusoidal: 49763 harmonic: 13597 Sorted by residual: dihedral pdb=" C4' G 13369 " pdb=" C3' G 13369 " pdb=" C2' G 13369 " pdb=" C1' G 13369 " ideal model delta sinusoidal sigma weight residual -35.00 33.82 -68.82 1 8.00e+00 1.56e-02 9.58e+01 dihedral pdb=" C4' U 11276 " pdb=" C3' U 11276 " pdb=" C2' U 11276 " pdb=" C1' U 11276 " ideal model delta sinusoidal sigma weight residual -35.00 33.39 -68.39 1 8.00e+00 1.56e-02 9.48e+01 dihedral pdb=" C5' G 13369 " pdb=" C4' G 13369 " pdb=" C3' G 13369 " pdb=" O3' G 13369 " ideal model delta sinusoidal sigma weight residual 147.00 79.37 67.63 1 8.00e+00 1.56e-02 9.29e+01 ... (remaining 63357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 13472 0.066 - 0.132: 620 0.132 - 0.198: 16 0.198 - 0.264: 27 0.264 - 0.330: 2 Chirality restraints: 14137 Sorted by residual: chirality pdb=" C3' G 13369 " pdb=" C4' G 13369 " pdb=" O3' G 13369 " pdb=" C2' G 13369 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C3' U 11276 " pdb=" C4' U 11276 " pdb=" O3' U 11276 " pdb=" C2' U 11276 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" P G 1 781 " pdb=" OP1 G 1 781 " pdb=" OP2 G 1 781 " pdb=" O5' G 1 781 " both_signs ideal model delta sigma weight residual True 2.41 -2.67 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 14134 not shown) Planarity restraints: 12712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER O 163 " 0.012 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C SER O 163 " -0.039 2.00e-02 2.50e+03 pdb=" O SER O 163 " 0.014 2.00e-02 2.50e+03 pdb=" N SER O 164 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 13 " 0.027 2.00e-02 2.50e+03 1.19e-02 4.62e+00 pdb=" N9 A 2 13 " -0.024 2.00e-02 2.50e+03 pdb=" C8 A 2 13 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A 2 13 " -0.009 2.00e-02 2.50e+03 pdb=" C5 A 2 13 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A 2 13 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A 2 13 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A 2 13 " 0.014 2.00e-02 2.50e+03 pdb=" C2 A 2 13 " -0.007 2.00e-02 2.50e+03 pdb=" N3 A 2 13 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A 2 13 " 0.002 2.00e-02 2.50e+03 pdb=" H8 A 2 13 " 0.005 2.00e-02 2.50e+03 pdb=" H2 A 2 13 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU S 14 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO S 15 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO S 15 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 15 " 0.029 5.00e-02 4.00e+02 ... (remaining 12709 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 4866 2.15 - 2.76: 198577 2.76 - 3.37: 336932 3.37 - 3.99: 455559 3.99 - 4.60: 683526 Nonbonded interactions: 1679460 Sorted by model distance: nonbonded pdb=" OP1 U 1 594 " pdb=" H1 G 1 609 " model vdw 1.537 1.850 nonbonded pdb=" O2' G 13149 " pdb=" H PHE B 130 " model vdw 1.540 1.850 nonbonded pdb=" OP1 C 11411 " pdb=" H HIS e 98 " model vdw 1.560 1.850 nonbonded pdb=" O SER B 187 " pdb=" H GLU B 190 " model vdw 1.567 1.850 nonbonded pdb=" OD1 ASN V 104 " pdb=" H GLU V 108 " model vdw 1.568 1.850 ... (remaining 1679455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.070 Extract box with map and model: 16.670 Check model and map are aligned: 1.300 Set scattering table: 0.820 Process input model: 362.880 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.280 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 389.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 76937 Z= 0.096 Angle : 0.438 10.296 112808 Z= 0.230 Chirality : 0.031 0.330 14137 Planarity : 0.002 0.052 7457 Dihedral : 22.637 179.635 41113 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.16 % Favored : 95.82 % Rotamer: Outliers : 0.61 % Allowed : 11.71 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.53 (0.14), residues: 3991 helix: 2.70 (0.14), residues: 1523 sheet: -0.27 (0.21), residues: 580 loop : 0.10 (0.15), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 60 HIS 0.004 0.000 HIS B 163 PHE 0.010 0.001 PHE b 278 TYR 0.014 0.001 TYR b 197 ARG 0.010 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 748 time to evaluate : 5.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 155 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9210 (tm) REVERT: G 111 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8876 (mmpt) REVERT: G 156 ASP cc_start: 0.6213 (p0) cc_final: 0.5976 (t0) REVERT: G 173 MET cc_start: 0.7431 (mmm) cc_final: 0.7099 (mmm) REVERT: H 9 GLN cc_start: 0.9365 (mt0) cc_final: 0.9148 (mp10) REVERT: H 11 GLU cc_start: 0.9166 (mp0) cc_final: 0.8718 (tm-30) REVERT: H 36 LYS cc_start: 0.9327 (ttmm) cc_final: 0.9109 (ttpt) REVERT: L 27 ASP cc_start: 0.9253 (p0) cc_final: 0.8975 (p0) REVERT: M 14 LEU cc_start: 0.8989 (mt) cc_final: 0.8569 (mt) REVERT: N 192 LYS cc_start: 0.9429 (tttt) cc_final: 0.9193 (tppt) REVERT: S 3 HIS cc_start: 0.8322 (t70) cc_final: 0.7928 (t70) REVERT: S 61 ILE cc_start: 0.9469 (tt) cc_final: 0.9227 (pt) REVERT: V 89 ASP cc_start: 0.8571 (t70) cc_final: 0.8213 (p0) REVERT: b 50 VAL cc_start: 0.8354 (t) cc_final: 0.8131 (p) REVERT: b 181 SER cc_start: 0.5959 (t) cc_final: 0.5685 (m) REVERT: b 208 HIS cc_start: 0.7836 (m-70) cc_final: 0.7604 (m90) REVERT: b 258 GLU cc_start: 0.9263 (tt0) cc_final: 0.9011 (tp30) REVERT: e 75 LEU cc_start: 0.9053 (tp) cc_final: 0.8833 (pt) REVERT: f 24 ASN cc_start: 0.8699 (t0) cc_final: 0.8370 (t0) REVERT: r 13 GLN cc_start: 0.8206 (mt0) cc_final: 0.8000 (mp10) REVERT: y 44 ASP cc_start: 0.8754 (m-30) cc_final: 0.8057 (p0) REVERT: y 53 ILE cc_start: 0.8475 (mm) cc_final: 0.7894 (tp) outliers start: 21 outliers final: 10 residues processed: 764 average time/residue: 1.6459 time to fit residues: 2010.8802 Evaluate side-chains 484 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 473 time to evaluate : 5.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain Y residue 37 LYS Chi-restraints excluded: chain b residue 278 PHE Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain y residue 173 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 578 random chunks: chunk 488 optimal weight: 5.9990 chunk 438 optimal weight: 30.0000 chunk 243 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 295 optimal weight: 20.0000 chunk 234 optimal weight: 7.9990 chunk 453 optimal weight: 1.9990 chunk 175 optimal weight: 20.0000 chunk 275 optimal weight: 7.9990 chunk 337 optimal weight: 8.9990 chunk 524 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 HIS B 121 ASN C 48 GLN C 291 ASN C 304 GLN F 209 ASN ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN L 103 ASN O 29 ASN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 ASN ** b 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 272 HIS f 42 GLN h 59 ASN j 48 ASN r 3 GLN r 49 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 76937 Z= 0.302 Angle : 0.614 10.280 112808 Z= 0.318 Chirality : 0.036 0.244 14137 Planarity : 0.004 0.059 7457 Dihedral : 23.592 179.169 32950 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.94 % Rotamer: Outliers : 1.76 % Allowed : 16.16 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3991 helix: 1.97 (0.13), residues: 1531 sheet: -0.40 (0.21), residues: 579 loop : -0.36 (0.15), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 106 HIS 0.028 0.002 HIS e 88 PHE 0.020 0.002 PHE Q 96 TYR 0.031 0.002 TYR P 47 ARG 0.013 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 459 time to evaluate : 5.050 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: C 99 MET cc_start: 0.8907 (ptm) cc_final: 0.8697 (ptt) REVERT: G 111 LYS cc_start: 0.9092 (mtpp) cc_final: 0.8883 (mmpt) REVERT: H 11 GLU cc_start: 0.9221 (mp0) cc_final: 0.8682 (tm-30) REVERT: L 27 ASP cc_start: 0.9380 (p0) cc_final: 0.9121 (p0) REVERT: M 35 ILE cc_start: 0.9703 (mt) cc_final: 0.9437 (tt) REVERT: N 188 ARG cc_start: 0.6343 (ptp-170) cc_final: 0.5937 (ptp-170) REVERT: N 192 LYS cc_start: 0.9454 (tttt) cc_final: 0.9210 (tppt) REVERT: Q 22 ASP cc_start: 0.9341 (m-30) cc_final: 0.8943 (t0) REVERT: S 43 TYR cc_start: 0.9320 (t80) cc_final: 0.9066 (t80) REVERT: b 258 GLU cc_start: 0.9272 (tt0) cc_final: 0.8991 (tp30) REVERT: e 75 LEU cc_start: 0.9108 (tp) cc_final: 0.8842 (pt) REVERT: f 33 GLU cc_start: 0.9425 (mt-10) cc_final: 0.9107 (pp20) REVERT: y 44 ASP cc_start: 0.8906 (m-30) cc_final: 0.8230 (p0) REVERT: y 53 ILE cc_start: 0.8525 (mm) cc_final: 0.8019 (tp) outliers start: 61 outliers final: 39 residues processed: 505 average time/residue: 1.5089 time to fit residues: 1216.2613 Evaluate side-chains 428 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 389 time to evaluate : 5.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 120 GLU Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain Y residue 37 LYS Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 64 ILE Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 278 PHE Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 83 GLU Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 40 SER Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain r residue 3 GLN Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 173 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 578 random chunks: chunk 291 optimal weight: 8.9990 chunk 162 optimal weight: 40.0000 chunk 436 optimal weight: 30.0000 chunk 357 optimal weight: 6.9990 chunk 144 optimal weight: 20.0000 chunk 525 optimal weight: 10.0000 chunk 568 optimal weight: 20.0000 chunk 468 optimal weight: 20.0000 chunk 521 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 421 optimal weight: 30.0000 overall best weight: 11.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN E 57 HIS F 186 HIS G 95 ASN H 51 GLN H 162 GLN ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN S 62 ASN S 74 ASN S 114 HIS S 138 GLN W 54 GLN W 205 GLN b 78 HIS e 88 HIS h 59 ASN ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 3 GLN ** y 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.139 76937 Z= 0.475 Angle : 0.746 10.001 112808 Z= 0.389 Chirality : 0.042 0.240 14137 Planarity : 0.006 0.068 7457 Dihedral : 24.283 179.739 32940 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 25.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.32 % Favored : 92.61 % Rotamer: Outliers : 3.18 % Allowed : 16.71 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.70 (0.13), residues: 3991 helix: 0.65 (0.13), residues: 1536 sheet: -0.99 (0.21), residues: 598 loop : -1.19 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 94 HIS 0.010 0.002 HIS F 222 PHE 0.027 0.002 PHE G 94 TYR 0.025 0.002 TYR b 205 ARG 0.008 0.001 ARG u 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 394 time to evaluate : 5.057 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: G 94 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7296 (t80) REVERT: H 11 GLU cc_start: 0.9254 (mp0) cc_final: 0.8660 (tm-30) REVERT: H 107 ASP cc_start: 0.9311 (OUTLIER) cc_final: 0.8607 (t70) REVERT: H 111 PHE cc_start: 0.8752 (m-80) cc_final: 0.8256 (m-10) REVERT: H 162 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8678 (tm-30) REVERT: H 171 ASP cc_start: 0.7739 (t0) cc_final: 0.7476 (t0) REVERT: L 27 ASP cc_start: 0.9549 (p0) cc_final: 0.9306 (p0) REVERT: M 62 GLN cc_start: 0.9193 (mp10) cc_final: 0.8934 (mp10) REVERT: M 107 GLU cc_start: 0.9557 (mt-10) cc_final: 0.9354 (mt-10) REVERT: N 192 LYS cc_start: 0.9552 (tttt) cc_final: 0.9340 (tppt) REVERT: Q 22 ASP cc_start: 0.9422 (m-30) cc_final: 0.9023 (t0) REVERT: V 57 MET cc_start: 0.5832 (ttp) cc_final: 0.5519 (tpp) REVERT: W 161 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7095 (pp) REVERT: b 284 MET cc_start: 0.7125 (ttm) cc_final: 0.6771 (tmm) REVERT: e 75 LEU cc_start: 0.9218 (tp) cc_final: 0.8852 (pt) REVERT: r 26 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7875 (mtpp) REVERT: y 44 ASP cc_start: 0.8952 (m-30) cc_final: 0.8228 (p0) REVERT: y 53 ILE cc_start: 0.8719 (mm) cc_final: 0.8224 (tp) outliers start: 110 outliers final: 77 residues processed: 486 average time/residue: 1.5891 time to fit residues: 1243.4335 Evaluate side-chains 435 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 353 time to evaluate : 5.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 117 ILE Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 120 GLU Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 17 GLU Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 108 GLN Chi-restraints excluded: chain S residue 117 ARG Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 161 LEU Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain Y residue 11 ASP Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 155 GLN Chi-restraints excluded: chain b residue 178 VAL Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 278 PHE Chi-restraints excluded: chain b residue 469 TYR Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 83 GLU Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain h residue 4 VAL Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain r residue 26 LYS Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain y residue 118 HIS Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 173 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 578 random chunks: chunk 519 optimal weight: 2.9990 chunk 395 optimal weight: 7.9990 chunk 272 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 250 optimal weight: 2.9990 chunk 353 optimal weight: 9.9990 chunk 527 optimal weight: 3.9990 chunk 558 optimal weight: 40.0000 chunk 275 optimal weight: 2.9990 chunk 500 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS C 59 GLN H 58 HIS O 31 GLN S 138 GLN V 81 GLN ** b 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 HIS e 49 ASN ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 76937 Z= 0.166 Angle : 0.527 7.281 112808 Z= 0.276 Chirality : 0.033 0.206 14137 Planarity : 0.004 0.059 7457 Dihedral : 24.107 178.555 32936 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.19 % Favored : 94.76 % Rotamer: Outliers : 1.73 % Allowed : 18.93 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.21 (0.13), residues: 3991 helix: 1.61 (0.13), residues: 1530 sheet: -0.82 (0.21), residues: 601 loop : -0.75 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 126 HIS 0.014 0.001 HIS S 49 PHE 0.016 0.001 PHE u 29 TYR 0.032 0.001 TYR h 70 ARG 0.005 0.000 ARG P 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 390 time to evaluate : 5.037 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: G 94 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7174 (t80) REVERT: H 11 GLU cc_start: 0.9281 (mp0) cc_final: 0.8691 (tm-30) REVERT: H 107 ASP cc_start: 0.9373 (OUTLIER) cc_final: 0.8715 (t70) REVERT: H 171 ASP cc_start: 0.7529 (t0) cc_final: 0.7136 (t0) REVERT: L 27 ASP cc_start: 0.9447 (p0) cc_final: 0.9192 (p0) REVERT: M 107 GLU cc_start: 0.9553 (mt-10) cc_final: 0.9327 (mt-10) REVERT: N 192 LYS cc_start: 0.9512 (tttt) cc_final: 0.9247 (tppt) REVERT: Q 22 ASP cc_start: 0.9358 (m-30) cc_final: 0.8857 (t0) REVERT: V 57 MET cc_start: 0.5788 (ttp) cc_final: 0.5474 (tpp) REVERT: V 126 TRP cc_start: 0.9170 (m100) cc_final: 0.8731 (m100) REVERT: b 284 MET cc_start: 0.7144 (ttm) cc_final: 0.6814 (tmm) REVERT: e 75 LEU cc_start: 0.9147 (tp) cc_final: 0.8914 (pt) REVERT: u 1 MET cc_start: 0.3677 (mtt) cc_final: 0.3366 (mtt) REVERT: y 1 MET cc_start: 0.7301 (mmt) cc_final: 0.7049 (mmt) REVERT: y 44 ASP cc_start: 0.8911 (m-30) cc_final: 0.8180 (p0) REVERT: y 53 ILE cc_start: 0.8660 (mm) cc_final: 0.8136 (tp) REVERT: y 162 HIS cc_start: 0.7726 (p-80) cc_final: 0.7270 (p-80) outliers start: 60 outliers final: 46 residues processed: 435 average time/residue: 1.4848 time to fit residues: 1028.3478 Evaluate side-chains 414 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 366 time to evaluate : 5.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 108 GLN Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 178 VAL Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 245 HIS Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 469 TYR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 83 GLU Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain h residue 4 VAL Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 173 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 578 random chunks: chunk 465 optimal weight: 30.0000 chunk 317 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 415 optimal weight: 9.9990 chunk 230 optimal weight: 1.9990 chunk 476 optimal weight: 30.0000 chunk 386 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 285 optimal weight: 8.9990 chunk 501 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN ** b 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 HIS e 98 HIS ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 62 GLN h 104 GLN ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 17 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 76937 Z= 0.295 Angle : 0.576 7.621 112808 Z= 0.302 Chirality : 0.036 0.230 14137 Planarity : 0.004 0.062 7457 Dihedral : 24.095 179.810 32934 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.97 % Favored : 92.98 % Rotamer: Outliers : 2.25 % Allowed : 19.31 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.07 (0.13), residues: 3991 helix: 1.40 (0.13), residues: 1529 sheet: -1.00 (0.21), residues: 605 loop : -0.91 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 99 HIS 0.011 0.001 HIS b 245 PHE 0.017 0.002 PHE b 77 TYR 0.016 0.001 TYR h 70 ARG 0.005 0.000 ARG P 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 374 time to evaluate : 4.611 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: G 94 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.7220 (t80) REVERT: H 11 GLU cc_start: 0.9263 (mp0) cc_final: 0.8647 (tm-30) REVERT: H 107 ASP cc_start: 0.9358 (OUTLIER) cc_final: 0.8860 (t70) REVERT: H 171 ASP cc_start: 0.7744 (t0) cc_final: 0.7422 (t0) REVERT: L 27 ASP cc_start: 0.9499 (p0) cc_final: 0.9264 (p0) REVERT: M 107 GLU cc_start: 0.9543 (mt-10) cc_final: 0.9321 (mt-10) REVERT: Q 22 ASP cc_start: 0.9405 (m-30) cc_final: 0.8981 (t0) REVERT: V 57 MET cc_start: 0.5648 (ttp) cc_final: 0.5372 (tpp) REVERT: b 284 MET cc_start: 0.7170 (ttm) cc_final: 0.6752 (tmm) REVERT: e 95 GLU cc_start: 0.8864 (tt0) cc_final: 0.8504 (pp20) REVERT: j 75 LYS cc_start: 0.9246 (tptp) cc_final: 0.9014 (tptp) REVERT: u 1 MET cc_start: 0.4032 (mtt) cc_final: 0.3776 (mtt) REVERT: y 1 MET cc_start: 0.6484 (mmt) cc_final: 0.6243 (mmt) REVERT: y 44 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8172 (p0) REVERT: y 53 ILE cc_start: 0.8701 (mm) cc_final: 0.8200 (tp) REVERT: y 162 HIS cc_start: 0.7611 (p-80) cc_final: 0.7168 (p-80) outliers start: 78 outliers final: 64 residues processed: 432 average time/residue: 1.4749 time to fit residues: 1019.0215 Evaluate side-chains 432 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 365 time to evaluate : 5.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 117 ILE Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 120 GLU Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 117 ARG Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 178 VAL Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 245 HIS Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 469 TYR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 83 GLU Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain h residue 4 VAL Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 44 ASP Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 173 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 578 random chunks: chunk 187 optimal weight: 9.9990 chunk 503 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 328 optimal weight: 10.0000 chunk 137 optimal weight: 30.0000 chunk 559 optimal weight: 7.9990 chunk 464 optimal weight: 20.0000 chunk 258 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 chunk 293 optimal weight: 10.0000 overall best weight: 7.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN P 64 ASN ** b 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 7 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 76937 Z= 0.306 Angle : 0.588 8.723 112808 Z= 0.310 Chirality : 0.036 0.256 14137 Planarity : 0.004 0.064 7457 Dihedral : 24.235 179.308 32934 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.24 % Favored : 92.71 % Rotamer: Outliers : 2.75 % Allowed : 19.34 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.13), residues: 3991 helix: 1.19 (0.13), residues: 1527 sheet: -1.10 (0.21), residues: 597 loop : -1.08 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 99 HIS 0.047 0.002 HIS b 245 PHE 0.020 0.002 PHE b 77 TYR 0.013 0.001 TYR u 4 ARG 0.008 0.001 ARG u 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 361 time to evaluate : 5.024 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: H 11 GLU cc_start: 0.9268 (mp0) cc_final: 0.8702 (tm-30) REVERT: H 107 ASP cc_start: 0.9347 (OUTLIER) cc_final: 0.8897 (t70) REVERT: H 171 ASP cc_start: 0.7946 (t0) cc_final: 0.7582 (t0) REVERT: L 27 ASP cc_start: 0.9487 (p0) cc_final: 0.9241 (p0) REVERT: M 107 GLU cc_start: 0.9556 (mt-10) cc_final: 0.9342 (mt-10) REVERT: O 187 GLU cc_start: 0.8198 (tp30) cc_final: 0.7967 (tp30) REVERT: P 154 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8262 (tp30) REVERT: V 57 MET cc_start: 0.5670 (ttp) cc_final: 0.5341 (tpp) REVERT: b 284 MET cc_start: 0.7028 (ttm) cc_final: 0.6574 (tmm) REVERT: e 95 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8529 (pp20) REVERT: u 1 MET cc_start: 0.4193 (mtt) cc_final: 0.3932 (mtt) REVERT: u 79 VAL cc_start: 0.3859 (OUTLIER) cc_final: 0.3604 (m) REVERT: u 93 MET cc_start: 0.6850 (mtt) cc_final: 0.6582 (mtt) REVERT: y 44 ASP cc_start: 0.8953 (m-30) cc_final: 0.8225 (p0) REVERT: y 53 ILE cc_start: 0.8709 (mm) cc_final: 0.8187 (tp) REVERT: y 162 HIS cc_start: 0.7690 (p-80) cc_final: 0.7269 (p-80) outliers start: 95 outliers final: 76 residues processed: 433 average time/residue: 1.5741 time to fit residues: 1102.3935 Evaluate side-chains 422 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 343 time to evaluate : 5.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 117 ILE Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 117 ARG Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 155 GLN Chi-restraints excluded: chain b residue 178 VAL Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 245 HIS Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 278 PHE Chi-restraints excluded: chain b residue 469 TYR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 83 GLU Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 173 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 578 random chunks: chunk 539 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 318 optimal weight: 9.9990 chunk 408 optimal weight: 1.9990 chunk 316 optimal weight: 7.9990 chunk 470 optimal weight: 30.0000 chunk 312 optimal weight: 20.0000 chunk 557 optimal weight: 10.0000 chunk 348 optimal weight: 6.9990 chunk 339 optimal weight: 9.9990 chunk 257 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN ** b 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 76937 Z= 0.311 Angle : 0.596 9.422 112808 Z= 0.312 Chirality : 0.036 0.263 14137 Planarity : 0.004 0.066 7457 Dihedral : 24.306 179.890 32934 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.47 % Favored : 92.48 % Rotamer: Outliers : 2.86 % Allowed : 19.16 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 3991 helix: 1.13 (0.13), residues: 1525 sheet: -1.12 (0.21), residues: 573 loop : -1.20 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP b 5 HIS 0.033 0.002 HIS b 245 PHE 0.021 0.002 PHE G 91 TYR 0.014 0.002 TYR f 51 ARG 0.015 0.000 ARG h 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 354 time to evaluate : 5.019 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: H 11 GLU cc_start: 0.9275 (mp0) cc_final: 0.8938 (tm-30) REVERT: H 19 SER cc_start: 0.9294 (OUTLIER) cc_final: 0.8760 (t) REVERT: H 107 ASP cc_start: 0.9332 (OUTLIER) cc_final: 0.8883 (t70) REVERT: H 171 ASP cc_start: 0.7947 (t0) cc_final: 0.7553 (t0) REVERT: L 27 ASP cc_start: 0.9468 (p0) cc_final: 0.9165 (p0) REVERT: M 107 GLU cc_start: 0.9558 (mt-10) cc_final: 0.9347 (mt-10) REVERT: O 187 GLU cc_start: 0.8218 (tp30) cc_final: 0.8006 (tp30) REVERT: P 154 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8265 (tp30) REVERT: V 23 MET cc_start: 0.4060 (pmm) cc_final: 0.3370 (ppp) REVERT: V 57 MET cc_start: 0.5683 (ttp) cc_final: 0.5385 (tpp) REVERT: b 278 PHE cc_start: 0.6438 (OUTLIER) cc_final: 0.6231 (p90) REVERT: b 284 MET cc_start: 0.7200 (ttm) cc_final: 0.6720 (tmm) REVERT: u 1 MET cc_start: 0.4387 (mtt) cc_final: 0.4180 (mtt) REVERT: u 93 MET cc_start: 0.6808 (mtt) cc_final: 0.6521 (mtt) REVERT: y 44 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8277 (p0) REVERT: y 151 TYR cc_start: 0.6807 (m-80) cc_final: 0.6375 (m-80) REVERT: y 162 HIS cc_start: 0.7690 (p-80) cc_final: 0.7240 (p-80) outliers start: 99 outliers final: 84 residues processed: 433 average time/residue: 1.4387 time to fit residues: 1004.1196 Evaluate side-chains 433 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 344 time to evaluate : 5.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 120 GLU Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 117 ARG Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 158 ILE Chi-restraints excluded: chain W residue 220 TYR Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 155 GLN Chi-restraints excluded: chain b residue 178 VAL Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 278 PHE Chi-restraints excluded: chain b residue 469 TYR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 83 GLU Chi-restraints excluded: chain e residue 120 THR Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 70 LYS Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 44 ASP Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 173 LEU Chi-restraints excluded: chain y residue 224 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 578 random chunks: chunk 344 optimal weight: 8.9990 chunk 222 optimal weight: 7.9990 chunk 332 optimal weight: 9.9990 chunk 167 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 354 optimal weight: 1.9990 chunk 379 optimal weight: 20.0000 chunk 275 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 437 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 ASN ** b 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 HIS ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 76937 Z= 0.299 Angle : 0.589 7.717 112808 Z= 0.309 Chirality : 0.036 0.265 14137 Planarity : 0.004 0.068 7457 Dihedral : 24.359 179.599 32934 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.19 % Favored : 92.76 % Rotamer: Outliers : 2.75 % Allowed : 19.62 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.54 (0.13), residues: 3991 helix: 1.07 (0.13), residues: 1530 sheet: -1.31 (0.20), residues: 605 loop : -1.22 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP V 126 HIS 0.014 0.001 HIS b 245 PHE 0.020 0.002 PHE b 77 TYR 0.012 0.001 TYR Q 33 ARG 0.011 0.000 ARG P 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 354 time to evaluate : 5.065 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: H 11 GLU cc_start: 0.9343 (mp0) cc_final: 0.8938 (tm-30) REVERT: H 19 SER cc_start: 0.9319 (OUTLIER) cc_final: 0.8789 (t) REVERT: H 107 ASP cc_start: 0.9299 (OUTLIER) cc_final: 0.8903 (t70) REVERT: H 171 ASP cc_start: 0.7994 (t0) cc_final: 0.7602 (t0) REVERT: L 27 ASP cc_start: 0.9461 (p0) cc_final: 0.9156 (p0) REVERT: O 138 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8319 (tt) REVERT: O 187 GLU cc_start: 0.8191 (tp30) cc_final: 0.7949 (tp30) REVERT: P 154 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8315 (tp30) REVERT: V 57 MET cc_start: 0.5734 (ttp) cc_final: 0.5406 (tpp) REVERT: V 126 TRP cc_start: 0.9142 (m100) cc_final: 0.8918 (m100) REVERT: b 278 PHE cc_start: 0.6379 (OUTLIER) cc_final: 0.6170 (p90) REVERT: b 284 MET cc_start: 0.7262 (ttm) cc_final: 0.6796 (tmm) REVERT: u 93 MET cc_start: 0.6959 (mtt) cc_final: 0.6710 (mtt) REVERT: y 44 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8279 (p0) REVERT: y 151 TYR cc_start: 0.6817 (m-80) cc_final: 0.6414 (m-80) REVERT: y 162 HIS cc_start: 0.7682 (p-80) cc_final: 0.7226 (p-80) outliers start: 95 outliers final: 80 residues processed: 426 average time/residue: 1.5520 time to fit residues: 1072.8916 Evaluate side-chains 431 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 345 time to evaluate : 4.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 117 ARG Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 220 TYR Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 155 GLN Chi-restraints excluded: chain b residue 178 VAL Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 278 PHE Chi-restraints excluded: chain b residue 469 TYR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 83 GLU Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 70 LYS Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 44 ASP Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 173 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 578 random chunks: chunk 506 optimal weight: 0.0980 chunk 533 optimal weight: 9.9990 chunk 486 optimal weight: 9.9990 chunk 519 optimal weight: 9.9990 chunk 312 optimal weight: 20.0000 chunk 226 optimal weight: 9.9990 chunk 407 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 469 optimal weight: 8.9990 chunk 491 optimal weight: 20.0000 chunk 517 optimal weight: 0.5980 overall best weight: 5.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 76937 Z= 0.261 Angle : 0.566 7.662 112808 Z= 0.297 Chirality : 0.035 0.265 14137 Planarity : 0.004 0.068 7457 Dihedral : 24.354 179.731 32934 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.27 % Favored : 92.68 % Rotamer: Outliers : 2.43 % Allowed : 20.17 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 3991 helix: 1.20 (0.13), residues: 1528 sheet: -1.32 (0.20), residues: 602 loop : -1.17 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP b 5 HIS 0.009 0.001 HIS O 72 PHE 0.016 0.001 PHE h 111 TYR 0.017 0.001 TYR G 177 ARG 0.012 0.000 ARG P 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 351 time to evaluate : 5.059 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: B 156 SER cc_start: 0.8010 (p) cc_final: 0.7667 (p) REVERT: H 2 LYS cc_start: 0.9108 (mttt) cc_final: 0.8845 (mttt) REVERT: H 11 GLU cc_start: 0.9246 (mp0) cc_final: 0.8935 (tm-30) REVERT: H 19 SER cc_start: 0.9349 (OUTLIER) cc_final: 0.8854 (t) REVERT: H 107 ASP cc_start: 0.9351 (m-30) cc_final: 0.8914 (t70) REVERT: H 171 ASP cc_start: 0.7990 (t0) cc_final: 0.7587 (t0) REVERT: L 27 ASP cc_start: 0.9451 (p0) cc_final: 0.9139 (p0) REVERT: P 154 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8325 (tp30) REVERT: V 57 MET cc_start: 0.5711 (ttp) cc_final: 0.5410 (tpp) REVERT: b 284 MET cc_start: 0.7260 (ttm) cc_final: 0.6797 (tmm) REVERT: u 93 MET cc_start: 0.6980 (mtt) cc_final: 0.6772 (mtt) REVERT: y 44 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8331 (p0) REVERT: y 151 TYR cc_start: 0.6799 (m-80) cc_final: 0.6369 (m-80) REVERT: y 162 HIS cc_start: 0.7635 (p-80) cc_final: 0.7160 (p-80) outliers start: 84 outliers final: 75 residues processed: 416 average time/residue: 1.4871 time to fit residues: 996.0405 Evaluate side-chains 424 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 346 time to evaluate : 5.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 117 ARG Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 220 TYR Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 155 GLN Chi-restraints excluded: chain b residue 178 VAL Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 469 TYR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 83 GLU Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 70 LYS Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 44 ASP Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain y residue 153 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 578 random chunks: chunk 340 optimal weight: 10.0000 chunk 548 optimal weight: 8.9990 chunk 335 optimal weight: 8.9990 chunk 260 optimal weight: 8.9990 chunk 381 optimal weight: 6.9990 chunk 575 optimal weight: 9.9990 chunk 529 optimal weight: 0.3980 chunk 458 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 354 optimal weight: 6.9990 chunk 281 optimal weight: 4.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 76937 Z= 0.191 Angle : 0.533 7.623 112808 Z= 0.279 Chirality : 0.034 0.268 14137 Planarity : 0.004 0.070 7457 Dihedral : 24.270 179.533 32932 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.86 % Favored : 94.11 % Rotamer: Outliers : 2.08 % Allowed : 20.58 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.18 (0.13), residues: 3991 helix: 1.45 (0.14), residues: 1528 sheet: -1.26 (0.20), residues: 597 loop : -1.04 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP V 126 HIS 0.007 0.001 HIS O 72 PHE 0.016 0.001 PHE G 91 TYR 0.017 0.001 TYR r 55 ARG 0.013 0.000 ARG P 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 356 time to evaluate : 5.021 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: B 156 SER cc_start: 0.8032 (p) cc_final: 0.7702 (p) REVERT: H 2 LYS cc_start: 0.9109 (mttt) cc_final: 0.8847 (mttt) REVERT: H 11 GLU cc_start: 0.9178 (mp0) cc_final: 0.8903 (tm-30) REVERT: H 19 SER cc_start: 0.9360 (OUTLIER) cc_final: 0.8913 (t) REVERT: H 107 ASP cc_start: 0.9323 (m-30) cc_final: 0.8898 (t70) REVERT: H 111 PHE cc_start: 0.8664 (m-80) cc_final: 0.8242 (m-80) REVERT: H 171 ASP cc_start: 0.7984 (t0) cc_final: 0.7661 (t0) REVERT: L 27 ASP cc_start: 0.9408 (p0) cc_final: 0.9081 (p0) REVERT: V 57 MET cc_start: 0.5717 (ttp) cc_final: 0.5409 (tpp) REVERT: V 120 LYS cc_start: 0.7036 (tptt) cc_final: 0.6648 (mmtp) REVERT: b 284 MET cc_start: 0.7252 (ttm) cc_final: 0.6826 (tmm) REVERT: r 10 HIS cc_start: 0.8589 (t-90) cc_final: 0.8346 (m-70) REVERT: u 79 VAL cc_start: 0.4341 (OUTLIER) cc_final: 0.4078 (m) REVERT: y 44 ASP cc_start: 0.8907 (m-30) cc_final: 0.8317 (p0) REVERT: y 151 TYR cc_start: 0.6777 (m-80) cc_final: 0.6354 (m-80) REVERT: y 162 HIS cc_start: 0.7700 (p-80) cc_final: 0.7213 (p-80) outliers start: 72 outliers final: 64 residues processed: 415 average time/residue: 1.5255 time to fit residues: 1023.9587 Evaluate side-chains 412 residues out of total 3460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 346 time to evaluate : 4.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 117 ARG Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 220 TYR Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 155 GLN Chi-restraints excluded: chain b residue 178 VAL Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 469 TYR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 83 GLU Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 70 LYS Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 153 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 578 random chunks: chunk 364 optimal weight: 9.9990 chunk 488 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 422 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 459 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 471 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 84 optimal weight: 30.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 98 ASN ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 48 ASN ** 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 = 0.3622 r_free = 0.3622 target = 0.060897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.045567 restraints weight = 1705941.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.046600 restraints weight = 692713.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.047136 restraints weight = 447753.980| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 76937 Z= 0.394 Angle : 0.650 7.593 112808 Z= 0.340 Chirality : 0.038 0.275 14137 Planarity : 0.005 0.070 7457 Dihedral : 24.432 179.981 32932 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.57 % Favored : 91.38 % Rotamer: Outliers : 2.40 % Allowed : 20.40 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.81 (0.13), residues: 3991 helix: 0.86 (0.13), residues: 1528 sheet: -1.47 (0.20), residues: 589 loop : -1.38 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP V 126 HIS 0.010 0.002 HIS O 72 PHE 0.017 0.002 PHE G 91 TYR 0.017 0.002 TYR H 3 ARG 0.013 0.001 ARG P 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29126.02 seconds wall clock time: 503 minutes 58.40 seconds (30238.40 seconds total)