Starting phenix.real_space_refine on Tue Mar 19 15:40:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/03_2024/6he5_0210.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/03_2024/6he5_0210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/03_2024/6he5_0210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/03_2024/6he5_0210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/03_2024/6he5_0210.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/03_2024/6he5_0210.pdb" } resolution = 4.12 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 15633 2.51 5 N 4127 2.21 5 O 4776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 18": "OD1" <-> "OD2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A ASP 90": "OD1" <-> "OD2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A ASP 187": "OD1" <-> "OD2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 217": "OD1" <-> "OD2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B ASP 18": "OD1" <-> "OD2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 151": "OD1" <-> "OD2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 241": "NH1" <-> "NH2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "C ASP 18": "OD1" <-> "OD2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 142": "OD1" <-> "OD2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C ASP 217": "OD1" <-> "OD2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C ARG 235": "NH1" <-> "NH2" Residue "C ARG 241": "NH1" <-> "NH2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "D ASP 9": "OD1" <-> "OD2" Residue "D ARG 10": "NH1" <-> "NH2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "D TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 151": "OD1" <-> "OD2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D ASP 187": "OD1" <-> "OD2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D ARG 241": "NH1" <-> "NH2" Residue "E ASP 18": "OD1" <-> "OD2" Residue "E PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "E ASP 104": "OD1" <-> "OD2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 149": "OE1" <-> "OE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E ARG 180": "NH1" <-> "NH2" Residue "E ASP 181": "OD1" <-> "OD2" Residue "E PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 186": "OD1" <-> "OD2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "E ASP 217": "OD1" <-> "OD2" Residue "E ASP 218": "OD1" <-> "OD2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E ARG 241": "NH1" <-> "NH2" Residue "F ASP 18": "OD1" <-> "OD2" Residue "F PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F ASP 90": "OD1" <-> "OD2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ASP 104": "OD1" <-> "OD2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F GLU 143": "OE1" <-> "OE2" Residue "F ASP 151": "OD1" <-> "OD2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "F ARG 180": "NH1" <-> "NH2" Residue "F ASP 186": "OD1" <-> "OD2" Residue "F ASP 187": "OD1" <-> "OD2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F GLU 207": "OE1" <-> "OE2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 235": "NH1" <-> "NH2" Residue "F ARG 241": "NH1" <-> "NH2" Residue "F GLU 242": "OE1" <-> "OE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 18": "OD1" <-> "OD2" Residue "G TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G ASP 51": "OD1" <-> "OD2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ASP 62": "OD1" <-> "OD2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "G ASP 104": "OD1" <-> "OD2" Residue "G ASP 118": "OD1" <-> "OD2" Residue "G PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "G ARG 180": "NH1" <-> "NH2" Residue "G ASP 181": "OD1" <-> "OD2" Residue "G ASP 182": "OD1" <-> "OD2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G GLU 210": "OE1" <-> "OE2" Residue "G TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 217": "OD1" <-> "OD2" Residue "G ASP 218": "OD1" <-> "OD2" Residue "G GLU 227": "OE1" <-> "OE2" Residue "G TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 234": "OE1" <-> "OE2" Residue "G ARG 235": "NH1" <-> "NH2" Residue "G GLU 238": "OE1" <-> "OE2" Residue "G ARG 241": "NH1" <-> "NH2" Residue "1 ASP 21": "OD1" <-> "OD2" Residue "1 GLU 28": "OE1" <-> "OE2" Residue "1 ARG 30": "NH1" <-> "NH2" Residue "1 ARG 51": "NH1" <-> "NH2" Residue "1 TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 80": "NH1" <-> "NH2" Residue "1 ARG 83": "NH1" <-> "NH2" Residue "1 ARG 88": "NH1" <-> "NH2" Residue "1 ARG 102": "NH1" <-> "NH2" Residue "1 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 116": "OD1" <-> "OD2" Residue "1 GLU 118": "OE1" <-> "OE2" Residue "1 TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 126": "OD1" <-> "OD2" Residue "1 GLU 152": "OE1" <-> "OE2" Residue "1 ASP 153": "OD1" <-> "OD2" Residue "1 ARG 154": "NH1" <-> "NH2" Residue "1 GLU 158": "OE1" <-> "OE2" Residue "1 ARG 170": "NH1" <-> "NH2" Residue "1 ASP 179": "OD1" <-> "OD2" Residue "1 ASP 194": "OD1" <-> "OD2" Residue "1 GLU 195": "OE1" <-> "OE2" Residue "1 PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 203": "OE1" <-> "OE2" Residue "1 GLU 205": "OE1" <-> "OE2" Residue "1 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 21": "OD1" <-> "OD2" Residue "2 GLU 28": "OE1" <-> "OE2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 50": "OD1" <-> "OD2" Residue "2 ARG 51": "NH1" <-> "NH2" Residue "2 ASP 62": "OD1" <-> "OD2" Residue "2 GLU 73": "OE1" <-> "OE2" Residue "2 ARG 80": "NH1" <-> "NH2" Residue "2 GLU 82": "OE1" <-> "OE2" Residue "2 ARG 83": "NH1" <-> "NH2" Residue "2 ARG 88": "NH1" <-> "NH2" Residue "2 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 102": "NH1" <-> "NH2" Residue "2 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 134": "OE1" <-> "OE2" Residue "2 TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 153": "OD1" <-> "OD2" Residue "2 ARG 154": "NH1" <-> "NH2" Residue "2 PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 158": "OE1" <-> "OE2" Residue "2 ASP 162": "OD1" <-> "OD2" Residue "2 GLU 163": "OE1" <-> "OE2" Residue "2 ARG 170": "NH1" <-> "NH2" Residue "2 ASP 187": "OD1" <-> "OD2" Residue "2 ASP 194": "OD1" <-> "OD2" Residue "2 PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 202": "OE1" <-> "OE2" Residue "2 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 30": "NH1" <-> "NH2" Residue "3 ASP 50": "OD1" <-> "OD2" Residue "3 ARG 51": "NH1" <-> "NH2" Residue "3 ASP 62": "OD1" <-> "OD2" Residue "3 ARG 80": "NH1" <-> "NH2" Residue "3 ARG 83": "NH1" <-> "NH2" Residue "3 ARG 88": "NH1" <-> "NH2" Residue "3 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 102": "NH1" <-> "NH2" Residue "3 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 136": "OD1" <-> "OD2" Residue "3 ASP 153": "OD1" <-> "OD2" Residue "3 ARG 154": "NH1" <-> "NH2" Residue "3 GLU 158": "OE1" <-> "OE2" Residue "3 ASP 162": "OD1" <-> "OD2" Residue "3 GLU 163": "OE1" <-> "OE2" Residue "3 ARG 170": "NH1" <-> "NH2" Residue "3 TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 184": "OD1" <-> "OD2" Residue "3 TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 202": "OE1" <-> "OE2" Residue "3 GLU 205": "OE1" <-> "OE2" Residue "3 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 21": "OD1" <-> "OD2" Residue "4 GLU 28": "OE1" <-> "OE2" Residue "4 ARG 30": "NH1" <-> "NH2" Residue "4 ASP 50": "OD1" <-> "OD2" Residue "4 ARG 51": "NH1" <-> "NH2" Residue "4 ARG 80": "NH1" <-> "NH2" Residue "4 ARG 83": "NH1" <-> "NH2" Residue "4 ARG 88": "NH1" <-> "NH2" Residue "4 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 102": "NH1" <-> "NH2" Residue "4 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 116": "OD1" <-> "OD2" Residue "4 TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 126": "OD1" <-> "OD2" Residue "4 ASP 136": "OD1" <-> "OD2" Residue "4 ARG 154": "NH1" <-> "NH2" Residue "4 GLU 158": "OE1" <-> "OE2" Residue "4 ARG 170": "NH1" <-> "NH2" Residue "4 TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 194": "OD1" <-> "OD2" Residue "4 PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 202": "OE1" <-> "OE2" Residue "4 GLU 203": "OE1" <-> "OE2" Residue "4 GLU 205": "OE1" <-> "OE2" Residue "4 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 30": "NH1" <-> "NH2" Residue "5 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 50": "OD1" <-> "OD2" Residue "5 ARG 51": "NH1" <-> "NH2" Residue "5 ASP 62": "OD1" <-> "OD2" Residue "5 TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 80": "NH1" <-> "NH2" Residue "5 ARG 83": "NH1" <-> "NH2" Residue "5 ARG 88": "NH1" <-> "NH2" Residue "5 ARG 102": "NH1" <-> "NH2" Residue "5 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 133": "OE1" <-> "OE2" Residue "5 ASP 136": "OD1" <-> "OD2" Residue "5 ARG 154": "NH1" <-> "NH2" Residue "5 GLU 158": "OE1" <-> "OE2" Residue "5 GLU 163": "OE1" <-> "OE2" Residue "5 ARG 170": "NH1" <-> "NH2" Residue "5 TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 184": "OD1" <-> "OD2" Residue "5 ASP 187": "OD1" <-> "OD2" Residue "5 GLU 193": "OE1" <-> "OE2" Residue "5 ASP 194": "OD1" <-> "OD2" Residue "5 PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 202": "OE1" <-> "OE2" Residue "5 GLU 205": "OE1" <-> "OE2" Residue "5 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 28": "OE1" <-> "OE2" Residue "6 ARG 30": "NH1" <-> "NH2" Residue "6 ARG 51": "NH1" <-> "NH2" Residue "6 GLU 73": "OE1" <-> "OE2" Residue "6 GLU 78": "OE1" <-> "OE2" Residue "6 ARG 80": "NH1" <-> "NH2" Residue "6 ARG 83": "NH1" <-> "NH2" Residue "6 ARG 88": "NH1" <-> "NH2" Residue "6 ARG 102": "NH1" <-> "NH2" Residue "6 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 153": "OD1" <-> "OD2" Residue "6 ARG 154": "NH1" <-> "NH2" Residue "6 GLU 166": "OE1" <-> "OE2" Residue "6 ARG 170": "NH1" <-> "NH2" Residue "6 ASP 179": "OD1" <-> "OD2" Residue "6 ASP 184": "OD1" <-> "OD2" Residue "6 ASP 187": "OD1" <-> "OD2" Residue "6 GLU 193": "OE1" <-> "OE2" Residue "6 ASP 194": "OD1" <-> "OD2" Residue "6 PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 203": "OE1" <-> "OE2" Residue "6 GLU 205": "OE1" <-> "OE2" Residue "6 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 28": "OE1" <-> "OE2" Residue "7 ARG 30": "NH1" <-> "NH2" Residue "7 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 50": "OD1" <-> "OD2" Residue "7 ARG 51": "NH1" <-> "NH2" Residue "7 GLU 78": "OE1" <-> "OE2" Residue "7 ARG 80": "NH1" <-> "NH2" Residue "7 GLU 82": "OE1" <-> "OE2" Residue "7 ARG 83": "NH1" <-> "NH2" Residue "7 ARG 88": "NH1" <-> "NH2" Residue "7 ARG 102": "NH1" <-> "NH2" Residue "7 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 116": "OD1" <-> "OD2" Residue "7 GLU 118": "OE1" <-> "OE2" Residue "7 TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 133": "OE1" <-> "OE2" Residue "7 ASP 136": "OD1" <-> "OD2" Residue "7 ARG 154": "NH1" <-> "NH2" Residue "7 GLU 158": "OE1" <-> "OE2" Residue "7 ASP 162": "OD1" <-> "OD2" Residue "7 GLU 166": "OE1" <-> "OE2" Residue "7 ARG 170": "NH1" <-> "NH2" Residue "7 ASP 179": "OD1" <-> "OD2" Residue "7 ASP 184": "OD1" <-> "OD2" Residue "7 ASP 187": "OD1" <-> "OD2" Residue "7 ASP 194": "OD1" <-> "OD2" Residue "7 PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 391": "OD1" <-> "OD2" Residue "H PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 391": "OD1" <-> "OD2" Residue "I PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 391": "OD1" <-> "OD2" Residue "L PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 391": "OD1" <-> "OD2" Residue "M PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 391": "OD1" <-> "OD2" Residue "J PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24633 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 8, 'TRANS': 230} Chain: "B" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain: "C" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain: "D" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 231} Chain: "E" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain: "F" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain: "G" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain: "1" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "2" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "3" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain: "4" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "5" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "6" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain: "7" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "H" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "K" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "L" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'TRANS': 6} Chain: "M" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'TRANS': 7} Time building chain proxies: 12.48, per 1000 atoms: 0.51 Number of scatterers: 24633 At special positions: 0 Unit cell: (131.32, 134, 108.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 4776 8.00 N 4127 7.00 C 15633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.78 Conformation dependent library (CDL) restraints added in 4.2 seconds 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5850 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 33 sheets defined 40.8% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 Processing helix chain 'A' and resid 28 through 34 removed outlier: 3.806A pdb=" N LYS A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 34' Processing helix chain 'A' and resid 81 through 103 removed outlier: 3.844A pdb=" N VAL A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 126 removed outlier: 3.561A pdb=" N LYS A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.801A pdb=" N GLU A 173 " --> pdb=" O ASN A 169 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 201 removed outlier: 3.518A pdb=" N ILE A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 225 through 244 removed outlier: 3.651A pdb=" N LYS A 230 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Proline residue: A 231 - end of helix removed outlier: 3.710A pdb=" N GLU A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 removed outlier: 3.513A pdb=" N VAL B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 104 removed outlier: 3.790A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.631A pdb=" N TYR B 123 " --> pdb=" O PHE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.584A pdb=" N GLU B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 201 Processing helix chain 'B' and resid 225 through 245 Proline residue: B 231 - end of helix removed outlier: 4.066A pdb=" N GLU B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 29 Processing helix chain 'C' and resid 81 through 103 removed outlier: 3.916A pdb=" N VAL C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 123 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.836A pdb=" N LYS C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 201 Processing helix chain 'C' and resid 225 through 244 removed outlier: 3.762A pdb=" N LYS C 230 " --> pdb=" O PRO C 226 " (cutoff:3.500A) Proline residue: C 231 - end of helix removed outlier: 3.638A pdb=" N ARG C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 81 through 103 removed outlier: 3.866A pdb=" N VAL D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 126 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.588A pdb=" N GLU D 173 " --> pdb=" O ASN D 169 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 201 removed outlier: 3.652A pdb=" N LEU D 198 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER D 199 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 200 " --> pdb=" O MET D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 225 through 243 Proline residue: D 231 - end of helix removed outlier: 3.659A pdb=" N ARG D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU D 238 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ARG D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.573A pdb=" N ARG E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 103 removed outlier: 3.578A pdb=" N ARG E 86 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.717A pdb=" N TYR E 123 " --> pdb=" O PHE E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 179 removed outlier: 3.969A pdb=" N LYS E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 201 removed outlier: 3.534A pdb=" N LEU E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 228 Processing helix chain 'E' and resid 229 through 244 removed outlier: 3.627A pdb=" N GLU E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG E 239 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 34 removed outlier: 3.877A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 104 removed outlier: 3.747A pdb=" N ARG F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.574A pdb=" N TYR F 123 " --> pdb=" O PHE F 119 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR F 124 " --> pdb=" O LYS F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 178 Processing helix chain 'F' and resid 184 through 201 Processing helix chain 'F' and resid 225 through 244 removed outlier: 3.597A pdb=" N LYS F 230 " --> pdb=" O PRO F 226 " (cutoff:3.500A) Proline residue: F 231 - end of helix removed outlier: 4.106A pdb=" N GLU F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG F 239 " --> pdb=" O ARG F 235 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.781A pdb=" N GLU G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 104 removed outlier: 3.889A pdb=" N VAL G 87 " --> pdb=" O ALA G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.758A pdb=" N TYR G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.843A pdb=" N LYS G 177 " --> pdb=" O GLU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 200 Processing helix chain 'G' and resid 229 through 246 removed outlier: 4.077A pdb=" N GLU G 238 " --> pdb=" O GLU G 234 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG G 239 " --> pdb=" O ARG G 235 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS G 246 " --> pdb=" O GLU G 242 " (cutoff:3.500A) Processing helix chain '1' and resid 59 through 82 removed outlier: 3.603A pdb=" N PHE 1 65 " --> pdb=" O GLY 1 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE 1 69 " --> pdb=" O PHE 1 65 " (cutoff:3.500A) Processing helix chain '1' and resid 86 through 101 removed outlier: 3.753A pdb=" N ILE 1 90 " --> pdb=" O THR 1 86 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER 1 95 " --> pdb=" O ALA 1 91 " (cutoff:3.500A) Processing helix chain '1' and resid 143 through 153 removed outlier: 4.660A pdb=" N GLY 1 149 " --> pdb=" O LEU 1 145 " (cutoff:3.500A) Processing helix chain '1' and resid 160 through 179 removed outlier: 3.608A pdb=" N GLU 1 166 " --> pdb=" O ASP 1 162 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP 1 179 " --> pdb=" O ALA 1 175 " (cutoff:3.500A) Processing helix chain '1' and resid 199 through 208 removed outlier: 4.326A pdb=" N GLU 1 203 " --> pdb=" O TYR 1 199 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN 1 206 " --> pdb=" O GLU 1 202 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE 1 207 " --> pdb=" O GLU 1 203 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU 1 208 " --> pdb=" O VAL 1 204 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 82 removed outlier: 3.711A pdb=" N ARG 2 68 " --> pdb=" O GLN 2 64 " (cutoff:3.500A) Processing helix chain '2' and resid 86 through 101 removed outlier: 3.669A pdb=" N ILE 2 90 " --> pdb=" O THR 2 86 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN 2 96 " --> pdb=" O THR 2 92 " (cutoff:3.500A) Processing helix chain '2' and resid 143 through 153 removed outlier: 3.596A pdb=" N ASP 2 153 " --> pdb=" O GLY 2 149 " (cutoff:3.500A) Processing helix chain '2' and resid 163 through 177 removed outlier: 3.950A pdb=" N LEU 2 167 " --> pdb=" O GLU 2 163 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS 2 177 " --> pdb=" O TYR 2 173 " (cutoff:3.500A) Processing helix chain '2' and resid 199 through 206 removed outlier: 4.225A pdb=" N GLU 2 203 " --> pdb=" O TYR 2 199 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL 2 204 " --> pdb=" O SER 2 200 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN 2 206 " --> pdb=" O GLU 2 202 " (cutoff:3.500A) Processing helix chain '3' and resid 59 through 82 removed outlier: 3.616A pdb=" N ALA 3 63 " --> pdb=" O SER 3 59 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE 3 69 " --> pdb=" O PHE 3 65 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE 3 70 " --> pdb=" O LEU 3 66 " (cutoff:3.500A) Processing helix chain '3' and resid 86 through 101 Processing helix chain '3' and resid 143 through 154 removed outlier: 4.111A pdb=" N GLY 3 149 " --> pdb=" O LEU 3 145 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL 3 150 " --> pdb=" O THR 3 146 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP 3 153 " --> pdb=" O GLY 3 149 " (cutoff:3.500A) Processing helix chain '3' and resid 160 through 176 removed outlier: 3.560A pdb=" N GLU 3 166 " --> pdb=" O ASP 3 162 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA 3 175 " --> pdb=" O ALA 3 171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET 3 176 " --> pdb=" O ILE 3 172 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 179 No H-bonds generated for 'chain '3' and resid 177 through 179' Processing helix chain '3' and resid 200 through 206 Processing helix chain '4' and resid 59 through 82 removed outlier: 3.709A pdb=" N ILE 4 69 " --> pdb=" O PHE 4 65 " (cutoff:3.500A) Processing helix chain '4' and resid 86 through 101 Processing helix chain '4' and resid 143 through 154 removed outlier: 3.790A pdb=" N VAL 4 150 " --> pdb=" O THR 4 146 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP 4 153 " --> pdb=" O GLY 4 149 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG 4 154 " --> pdb=" O VAL 4 150 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 177 removed outlier: 3.885A pdb=" N GLU 4 166 " --> pdb=" O ASP 4 162 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA 4 175 " --> pdb=" O ALA 4 171 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS 4 177 " --> pdb=" O TYR 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 199 through 209 removed outlier: 3.924A pdb=" N GLU 4 203 " --> pdb=" O TYR 4 199 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN 4 206 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE 4 207 " --> pdb=" O GLU 4 203 " (cutoff:3.500A) Processing helix chain '5' and resid 59 through 82 removed outlier: 3.605A pdb=" N ALA 5 63 " --> pdb=" O SER 5 59 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE 5 65 " --> pdb=" O GLY 5 61 " (cutoff:3.500A) Processing helix chain '5' and resid 86 through 101 Processing helix chain '5' and resid 143 through 152 removed outlier: 3.559A pdb=" N GLU 5 152 " --> pdb=" O TYR 5 148 " (cutoff:3.500A) Processing helix chain '5' and resid 160 through 177 removed outlier: 3.908A pdb=" N GLU 5 166 " --> pdb=" O ASP 5 162 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER 5 174 " --> pdb=" O ARG 5 170 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA 5 175 " --> pdb=" O ALA 5 171 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET 5 176 " --> pdb=" O ILE 5 172 " (cutoff:3.500A) Processing helix chain '5' and resid 179 through 184 removed outlier: 3.781A pdb=" N SER 5 182 " --> pdb=" O ASP 5 179 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP 5 184 " --> pdb=" O ALA 5 181 " (cutoff:3.500A) Processing helix chain '5' and resid 199 through 206 removed outlier: 4.443A pdb=" N GLU 5 203 " --> pdb=" O TYR 5 199 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL 5 204 " --> pdb=" O SER 5 200 " (cutoff:3.500A) Processing helix chain '6' and resid 59 through 82 removed outlier: 3.732A pdb=" N ILE 6 69 " --> pdb=" O PHE 6 65 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 101 removed outlier: 3.511A pdb=" N ILE 6 90 " --> pdb=" O THR 6 86 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER 6 100 " --> pdb=" O ASN 6 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR 6 101 " --> pdb=" O LEU 6 97 " (cutoff:3.500A) Processing helix chain '6' and resid 143 through 155 removed outlier: 3.630A pdb=" N GLY 6 149 " --> pdb=" O LEU 6 145 " (cutoff:3.500A) Processing helix chain '6' and resid 160 through 179 removed outlier: 3.506A pdb=" N ALA 6 164 " --> pdb=" O GLY 6 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU 6 166 " --> pdb=" O ASP 6 162 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE 6 172 " --> pdb=" O ALA 6 168 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS 6 177 " --> pdb=" O TYR 6 173 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG 6 178 " --> pdb=" O SER 6 174 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 208 removed outlier: 4.122A pdb=" N GLU 6 203 " --> pdb=" O TYR 6 199 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL 6 204 " --> pdb=" O SER 6 200 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN 6 206 " --> pdb=" O GLU 6 202 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE 6 207 " --> pdb=" O GLU 6 203 " (cutoff:3.500A) Processing helix chain '7' and resid 60 through 82 Processing helix chain '7' and resid 86 through 101 Processing helix chain '7' and resid 143 through 154 removed outlier: 3.800A pdb=" N GLY 7 149 " --> pdb=" O LEU 7 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL 7 150 " --> pdb=" O THR 7 146 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP 7 153 " --> pdb=" O GLY 7 149 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG 7 154 " --> pdb=" O VAL 7 150 " (cutoff:3.500A) Processing helix chain '7' and resid 163 through 177 removed outlier: 3.837A pdb=" N LEU 7 167 " --> pdb=" O GLU 7 163 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG 7 170 " --> pdb=" O GLU 7 166 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA 7 175 " --> pdb=" O ALA 7 171 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS 7 177 " --> pdb=" O TYR 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 199 through 205 removed outlier: 4.392A pdb=" N GLU 7 203 " --> pdb=" O TYR 7 199 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL 7 204 " --> pdb=" O SER 7 200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 164 removed outlier: 4.659A pdb=" N VAL A 211 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 removed outlier: 3.698A pdb=" N LEU A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 147 " --> pdb=" O TYR A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.575A pdb=" N GLY B 45 " --> pdb=" O CYS B 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 71 removed outlier: 6.219A pdb=" N ILE B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 147 " --> pdb=" O TYR B 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.836A pdb=" N GLY C 45 " --> pdb=" O CYS C 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 69 removed outlier: 4.152A pdb=" N LEU C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C 147 " --> pdb=" O TYR C 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 161 through 164 Processing sheet with id=AA8, first strand: chain 'D' and resid 68 through 69 removed outlier: 4.150A pdb=" N LEU D 147 " --> pdb=" O TYR D 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 161 through 164 removed outlier: 3.522A pdb=" N GLY E 45 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL E 211 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS E 215 " --> pdb=" O THR E 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.553A pdb=" N ALA E 77 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 161 through 164 removed outlier: 3.524A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL F 211 " --> pdb=" O VAL F 224 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 68 through 69 removed outlier: 3.565A pdb=" N LEU F 136 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU F 147 " --> pdb=" O TYR F 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 68 through 69 removed outlier: 4.857A pdb=" N GLY F 80 " --> pdb=" O VAL M 398 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 161 through 164 removed outlier: 3.521A pdb=" N ALA G 37 " --> pdb=" O ILE G 164 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY G 45 " --> pdb=" O CYS G 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 68 through 69 Processing sheet with id=AB7, first strand: chain 'G' and resid 68 through 69 removed outlier: 3.508A pdb=" N VAL L 398 " --> pdb=" O GLY G 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '1' and resid 139 through 141 Processing sheet with id=AB9, first strand: chain '1' and resid 32 through 33 Processing sheet with id=AC1, first strand: chain '1' and resid 45 through 49 removed outlier: 6.700A pdb=" N MET 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE 1 125 " --> pdb=" O LEU 1 110 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY 1 114 " --> pdb=" O SER 1 121 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER 1 121 " --> pdb=" O GLY 1 114 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE 1 122 " --> pdb=" O GLU 1 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '2' and resid 137 through 138 removed outlier: 3.651A pdb=" N ASP 2 187 " --> pdb=" O THR 2 27 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '2' and resid 32 through 33 Processing sheet with id=AC4, first strand: chain '2' and resid 45 through 49 removed outlier: 6.609A pdb=" N MET 2 52 " --> pdb=" O ILE 2 48 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU 2 110 " --> pdb=" O ILE 2 125 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE 2 122 " --> pdb=" O GLU 2 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '3' and resid 14 through 18 removed outlier: 3.540A pdb=" N ALA 3 26 " --> pdb=" O VAL 3 15 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET 3 25 " --> pdb=" O VAL 3 189 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP 3 187 " --> pdb=" O THR 3 27 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '3' and resid 46 through 49 removed outlier: 6.667A pdb=" N MET 3 52 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '4' and resid 137 through 138 removed outlier: 4.020A pdb=" N VAL 4 138 " --> pdb=" O GLY 4 16 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY 4 16 " --> pdb=" O VAL 4 138 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL 4 15 " --> pdb=" O ALA 4 26 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '4' and resid 46 through 49 removed outlier: 6.555A pdb=" N MET 4 52 " --> pdb=" O ILE 4 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '5' and resid 137 through 140 removed outlier: 3.637A pdb=" N ILE 5 191 " --> pdb=" O VAL 5 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '5' and resid 45 through 49 removed outlier: 6.742A pdb=" N MET 5 52 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER 5 121 " --> pdb=" O GLY 5 114 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE 5 122 " --> pdb=" O GLU 5 134 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE 5 132 " --> pdb=" O SER 5 124 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 14 through 18 removed outlier: 3.722A pdb=" N TYR 6 197 " --> pdb=" O LYS 6 190 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 31 through 33 removed outlier: 6.738A pdb=" N ALA 6 31 " --> pdb=" O ALA 6 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '6' and resid 45 through 49 removed outlier: 6.824A pdb=" N ILE 6 45 " --> pdb=" O THR 6 56 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR 6 56 " --> pdb=" O ILE 6 45 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN 6 47 " --> pdb=" O MET 6 54 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET 6 54 " --> pdb=" O GLN 6 47 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY 6 113 " --> pdb=" O ALA 6 53 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 6 110 " --> pdb=" O ILE 6 125 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE 6 122 " --> pdb=" O GLU 6 134 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '7' and resid 137 through 141 removed outlier: 5.394A pdb=" N THR 7 13 " --> pdb=" O GLU 7 28 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU 7 28 " --> pdb=" O THR 7 13 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY 7 22 " --> pdb=" O CYS 7 19 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL 7 23 " --> pdb=" O ILE 7 191 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '7' and resid 45 through 47 removed outlier: 3.549A pdb=" N ILE 7 122 " --> pdb=" O GLU 7 134 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE 7 132 " --> pdb=" O SER 7 124 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP 7 126 " --> pdb=" O GLY 7 130 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) 1273 hydrogen bonds defined for protein. 3699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.99 Time building geometry restraints manager: 9.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.23: 1776 1.23 - 1.46: 10918 1.46 - 1.69: 12100 1.69 - 1.92: 167 1.92 - 2.15: 7 Bond restraints: 24968 Sorted by residual: bond pdb=" CZ ARG 5 170 " pdb=" NH2 ARG 5 170 " ideal model delta sigma weight residual 1.330 2.147 -0.817 1.30e-02 5.92e+03 3.95e+03 bond pdb=" CG PHE 5 211 " pdb=" CD1 PHE 5 211 " ideal model delta sigma weight residual 1.384 2.104 -0.720 2.10e-02 2.27e+03 1.17e+03 bond pdb=" CG PHE 5 211 " pdb=" CD2 PHE 5 211 " ideal model delta sigma weight residual 1.384 2.041 -0.657 2.10e-02 2.27e+03 9.80e+02 bond pdb=" C LYS E 66 " pdb=" N ILE E 67 " ideal model delta sigma weight residual 1.330 1.710 -0.380 1.23e-02 6.61e+03 9.52e+02 bond pdb=" N GLN E 5 " pdb=" CA GLN E 5 " ideal model delta sigma weight residual 1.458 1.000 0.458 1.90e-02 2.77e+03 5.80e+02 ... (remaining 24963 not shown) Histogram of bond angle deviations from ideal: 86.98 - 97.93: 63 97.93 - 108.88: 4851 108.88 - 119.83: 18019 119.83 - 130.77: 10644 130.77 - 141.72: 83 Bond angle restraints: 33660 Sorted by residual: angle pdb=" NE ARG 5 170 " pdb=" CZ ARG 5 170 " pdb=" NH1 ARG 5 170 " ideal model delta sigma weight residual 121.50 101.39 20.11 1.00e+00 1.00e+00 4.05e+02 angle pdb=" N LYS 2 40 " pdb=" CA LYS 2 40 " pdb=" C LYS 2 40 " ideal model delta sigma weight residual 114.62 95.87 18.75 1.14e+00 7.69e-01 2.71e+02 angle pdb=" C GLU E 65 " pdb=" N LYS E 66 " pdb=" CA LYS E 66 " ideal model delta sigma weight residual 120.38 141.72 -21.34 1.37e+00 5.33e-01 2.43e+02 angle pdb=" CA LYS E 66 " pdb=" C LYS E 66 " pdb=" N ILE E 67 " ideal model delta sigma weight residual 117.22 101.99 15.23 1.17e+00 7.31e-01 1.69e+02 angle pdb=" O LYS E 66 " pdb=" C LYS E 66 " pdb=" N ILE E 67 " ideal model delta sigma weight residual 122.12 135.88 -13.76 1.06e+00 8.90e-01 1.69e+02 ... (remaining 33655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.08: 14375 25.08 - 50.16: 682 50.16 - 75.23: 224 75.23 - 100.31: 60 100.31 - 125.39: 2 Dihedral angle restraints: 15343 sinusoidal: 6204 harmonic: 9139 Sorted by residual: dihedral pdb=" CA GLU A 65 " pdb=" C GLU A 65 " pdb=" N LYS A 66 " pdb=" CA LYS A 66 " ideal model delta harmonic sigma weight residual -180.00 -54.61 -125.39 0 5.00e+00 4.00e-02 6.29e+02 dihedral pdb=" CA GLY H 394 " pdb=" C GLY H 394 " pdb=" N VAL H 395 " pdb=" CA VAL H 395 " ideal model delta harmonic sigma weight residual -180.00 -70.34 -109.66 0 5.00e+00 4.00e-02 4.81e+02 dihedral pdb=" CA ALA 2 139 " pdb=" C ALA 2 139 " pdb=" N THR 2 140 " pdb=" CA THR 2 140 " ideal model delta harmonic sigma weight residual 180.00 110.18 69.82 0 5.00e+00 4.00e-02 1.95e+02 ... (remaining 15340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 2874 0.225 - 0.450: 890 0.450 - 0.674: 107 0.674 - 0.899: 9 0.899 - 1.124: 1 Chirality restraints: 3881 Sorted by residual: chirality pdb=" CA THR 3 140 " pdb=" N THR 3 140 " pdb=" C THR 3 140 " pdb=" CB THR 3 140 " both_signs ideal model delta sigma weight residual False 2.53 1.40 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA ASP B 217 " pdb=" N ASP B 217 " pdb=" C ASP B 217 " pdb=" CB ASP B 217 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" CA GLU D 65 " pdb=" N GLU D 65 " pdb=" C GLU D 65 " pdb=" CB GLU D 65 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 3878 not shown) Planarity restraints: 4329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 5 199 " 0.225 2.00e-02 2.50e+03 1.45e-01 4.21e+02 pdb=" CG TYR 5 199 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR 5 199 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR 5 199 " -0.113 2.00e-02 2.50e+03 pdb=" CE1 TYR 5 199 " -0.166 2.00e-02 2.50e+03 pdb=" CE2 TYR 5 199 " -0.114 2.00e-02 2.50e+03 pdb=" CZ TYR 5 199 " 0.033 2.00e-02 2.50e+03 pdb=" OH TYR 5 199 " 0.231 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 123 " 0.214 2.00e-02 2.50e+03 1.28e-01 3.30e+02 pdb=" CG TYR G 123 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR G 123 " -0.114 2.00e-02 2.50e+03 pdb=" CD2 TYR G 123 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR G 123 " -0.079 2.00e-02 2.50e+03 pdb=" CE2 TYR G 123 " -0.121 2.00e-02 2.50e+03 pdb=" CZ TYR G 123 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR G 123 " 0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 3 101 " -0.196 2.00e-02 2.50e+03 1.26e-01 3.20e+02 pdb=" CG TYR 3 101 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR 3 101 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR 3 101 " 0.142 2.00e-02 2.50e+03 pdb=" CE1 TYR 3 101 " 0.139 2.00e-02 2.50e+03 pdb=" CE2 TYR 3 101 " 0.048 2.00e-02 2.50e+03 pdb=" CZ TYR 3 101 " 0.028 2.00e-02 2.50e+03 pdb=" OH TYR 3 101 " -0.209 2.00e-02 2.50e+03 ... (remaining 4326 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3223 2.77 - 3.30: 22758 3.30 - 3.83: 39960 3.83 - 4.37: 53183 4.37 - 4.90: 84967 Nonbonded interactions: 204091 Sorted by model distance: nonbonded pdb=" NH2 ARG 5 170 " pdb=" CD2 PHE 5 211 " model vdw 2.236 3.420 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CG PHE 5 211 " model vdw 2.237 3.340 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CE1 PHE 5 211 " model vdw 2.242 3.420 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CE2 PHE 5 211 " model vdw 2.250 3.420 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CZ PHE 5 211 " model vdw 2.251 3.420 ... (remaining 204086 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.850 Check model and map are aligned: 0.360 Set scattering table: 0.190 Process input model: 61.290 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 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 : 0.036 0.817 24968 Z= 2.339 Angle : 3.508 21.343 33660 Z= 2.349 Chirality : 0.204 1.124 3881 Planarity : 0.030 0.297 4329 Dihedral : 17.648 125.386 9493 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 2.18 % Allowed : 5.32 % Favored : 92.50 % Rotamer: Outliers : 4.51 % Allowed : 9.74 % Favored : 85.75 % Cbeta Deviations : 6.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 1.10 % Twisted General : 0.82 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.13), residues: 3122 helix: -1.29 (0.13), residues: 1197 sheet: -0.43 (0.20), residues: 563 loop : -2.82 (0.13), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.032 0.015 HIS G 73 PHE 0.189 0.040 PHE A 221 TYR 0.243 0.049 TYR F 8 ARG 0.091 0.012 ARG 1 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1303 time to evaluate : 2.828 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: A 111 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6469 (mm-30) REVERT: A 208 ASN cc_start: 0.7788 (p0) cc_final: 0.7355 (p0) REVERT: A 211 VAL cc_start: 0.7891 (t) cc_final: 0.7541 (p) REVERT: A 220 THR cc_start: 0.8239 (m) cc_final: 0.8001 (m) REVERT: B 24 VAL cc_start: 0.8283 (t) cc_final: 0.7918 (t) REVERT: B 152 PRO cc_start: 0.8929 (Cg_exo) cc_final: 0.8594 (Cg_endo) REVERT: B 208 ASN cc_start: 0.6638 (p0) cc_final: 0.6217 (p0) REVERT: C 23 GLN cc_start: 0.8418 (tp-100) cc_final: 0.8165 (tp40) REVERT: C 41 LYS cc_start: 0.8373 (ttpt) cc_final: 0.8068 (ttpt) REVERT: C 47 ILE cc_start: 0.8472 (mt) cc_final: 0.8268 (mt) REVERT: C 66 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8238 (tppt) REVERT: C 144 VAL cc_start: 0.8745 (m) cc_final: 0.8487 (m) REVERT: C 160 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7672 (mtpt) REVERT: D 82 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8625 (t) REVERT: D 89 ILE cc_start: 0.9190 (tp) cc_final: 0.8989 (tp) REVERT: D 115 LYS cc_start: 0.8472 (mttm) cc_final: 0.7842 (mttt) REVERT: D 121 GLN cc_start: 0.8060 (tm130) cc_final: 0.7739 (tm130) REVERT: D 174 PHE cc_start: 0.7339 (t80) cc_final: 0.6543 (t80) REVERT: D 211 VAL cc_start: 0.8980 (t) cc_final: 0.8740 (t) REVERT: E 25 GLU cc_start: 0.6352 (tp30) cc_final: 0.5641 (tp30) REVERT: E 41 LYS cc_start: 0.7779 (ttpt) cc_final: 0.7080 (ptmt) REVERT: E 49 ILE cc_start: 0.6840 (tt) cc_final: 0.6612 (tt) REVERT: E 68 TYR cc_start: 0.8023 (m-80) cc_final: 0.7711 (m-80) REVERT: E 116 ILE cc_start: 0.8525 (mt) cc_final: 0.8311 (mt) REVERT: E 120 LYS cc_start: 0.7119 (mttt) cc_final: 0.6897 (mttm) REVERT: E 186 ASP cc_start: 0.6779 (m-30) cc_final: 0.6126 (m-30) REVERT: E 235 ARG cc_start: 0.6204 (ttp-170) cc_final: 0.5559 (ttp80) REVERT: F 22 PHE cc_start: 0.6992 (m-80) cc_final: 0.6426 (m-80) REVERT: F 99 ASN cc_start: 0.7781 (t0) cc_final: 0.7479 (t0) REVERT: F 106 PRO cc_start: 0.9192 (Cg_exo) cc_final: 0.8719 (Cg_endo) REVERT: G 5 GLN cc_start: 0.4621 (OUTLIER) cc_final: 0.3614 (pm20) REVERT: G 16 SER cc_start: 0.7584 (p) cc_final: 0.7164 (p) REVERT: G 23 GLN cc_start: 0.8436 (tp-100) cc_final: 0.7965 (tp40) REVERT: G 47 ILE cc_start: 0.8519 (mt) cc_final: 0.7807 (mt) REVERT: G 157 LEU cc_start: 0.7984 (mt) cc_final: 0.7609 (mt) REVERT: G 171 VAL cc_start: 0.5969 (t) cc_final: 0.4258 (t) REVERT: G 200 ILE cc_start: 0.7751 (pt) cc_final: 0.7388 (pt) REVERT: G 224 VAL cc_start: 0.6674 (t) cc_final: 0.6304 (t) REVERT: 1 107 LEU cc_start: -0.0329 (OUTLIER) cc_final: -0.0710 (pt) REVERT: 2 44 LYS cc_start: 0.3812 (OUTLIER) cc_final: 0.3402 (mptm) REVERT: 2 162 ASP cc_start: 0.4157 (m-30) cc_final: 0.3663 (m-30) REVERT: 3 46 TYR cc_start: 0.7226 (m-80) cc_final: 0.6548 (m-80) REVERT: 3 93 LEU cc_start: 0.8152 (tp) cc_final: 0.7541 (tt) REVERT: 4 70 ILE cc_start: 0.9169 (mt) cc_final: 0.8903 (mt) REVERT: 5 146 THR cc_start: 0.6265 (p) cc_final: 0.5914 (p) REVERT: 6 155 PHE cc_start: 0.3192 (t80) cc_final: 0.2981 (t80) outliers start: 118 outliers final: 19 residues processed: 1361 average time/residue: 0.4186 time to fit residues: 837.1213 Evaluate side-chains 1112 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1088 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 241 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 279 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN F 237 ASN G 5 GLN G 97 GLN G 99 ASN 1 64 GLN 3 96 ASN 4 99 ASN 7 109 GLN 7 198 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 24968 Z= 0.351 Angle : 0.864 14.041 33660 Z= 0.472 Chirality : 0.051 0.233 3881 Planarity : 0.006 0.062 4329 Dihedral : 6.520 55.933 3498 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.65 % Favored : 96.03 % Rotamer: Outliers : 0.31 % Allowed : 4.59 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3122 helix: -0.05 (0.14), residues: 1242 sheet: 0.15 (0.19), residues: 590 loop : -2.11 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS E 73 PHE 0.029 0.003 PHE 4 155 TYR 0.038 0.003 TYR 6 46 ARG 0.012 0.001 ARG 5 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1301 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1293 time to evaluate : 2.723 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: A 121 GLN cc_start: 0.8560 (tp40) cc_final: 0.7696 (tm-30) REVERT: A 182 ASP cc_start: 0.5715 (p0) cc_final: 0.5484 (p0) REVERT: A 208 ASN cc_start: 0.7807 (p0) cc_final: 0.7547 (p0) REVERT: A 211 VAL cc_start: 0.8210 (t) cc_final: 0.7082 (p) REVERT: A 242 GLU cc_start: 0.6168 (mm-30) cc_final: 0.5954 (mm-30) REVERT: B 104 ASP cc_start: 0.7126 (m-30) cc_final: 0.6871 (m-30) REVERT: B 176 GLU cc_start: 0.6426 (mm-30) cc_final: 0.6160 (mm-30) REVERT: B 181 ASP cc_start: 0.7315 (m-30) cc_final: 0.6824 (m-30) REVERT: B 186 ASP cc_start: 0.6856 (p0) cc_final: 0.6475 (p0) REVERT: B 201 GLU cc_start: 0.5857 (tm-30) cc_final: 0.5302 (tm-30) REVERT: B 208 ASN cc_start: 0.6570 (p0) cc_final: 0.6098 (p0) REVERT: B 229 LEU cc_start: 0.7714 (mt) cc_final: 0.7440 (mt) REVERT: C 41 LYS cc_start: 0.8721 (ttpt) cc_final: 0.8472 (tttt) REVERT: C 137 LEU cc_start: 0.8767 (mt) cc_final: 0.8340 (mt) REVERT: C 149 GLU cc_start: 0.8176 (tt0) cc_final: 0.7868 (tt0) REVERT: C 160 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7635 (mtmm) REVERT: C 164 ILE cc_start: 0.9273 (pt) cc_final: 0.9041 (pt) REVERT: C 199 SER cc_start: 0.8840 (p) cc_final: 0.8163 (t) REVERT: C 202 SER cc_start: 0.7900 (p) cc_final: 0.7275 (p) REVERT: C 208 ASN cc_start: 0.7284 (p0) cc_final: 0.6945 (p0) REVERT: C 214 VAL cc_start: 0.8504 (t) cc_final: 0.8167 (t) REVERT: C 217 ASP cc_start: 0.7317 (p0) cc_final: 0.6859 (p0) REVERT: D 64 ILE cc_start: 0.7157 (pt) cc_final: 0.6931 (pt) REVERT: D 82 VAL cc_start: 0.8492 (t) cc_final: 0.8274 (t) REVERT: D 95 GLU cc_start: 0.7306 (tt0) cc_final: 0.6663 (tt0) REVERT: D 185 PHE cc_start: 0.6455 (t80) cc_final: 0.6105 (t80) REVERT: E 28 ARG cc_start: 0.7798 (mmm-85) cc_final: 0.7470 (mmm-85) REVERT: E 68 TYR cc_start: 0.8459 (m-80) cc_final: 0.8130 (m-80) REVERT: E 120 LYS cc_start: 0.8140 (mttt) cc_final: 0.7767 (mttm) REVERT: E 185 PHE cc_start: 0.8082 (t80) cc_final: 0.7869 (t80) REVERT: F 9 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8230 (p0) REVERT: F 26 TYR cc_start: 0.8681 (m-10) cc_final: 0.8214 (m-10) REVERT: F 150 THR cc_start: 0.7594 (p) cc_final: 0.7231 (p) REVERT: F 196 MET cc_start: 0.7390 (tpp) cc_final: 0.6873 (tpp) REVERT: F 199 SER cc_start: 0.8436 (p) cc_final: 0.7789 (t) REVERT: F 203 GLU cc_start: 0.7952 (pm20) cc_final: 0.7657 (pt0) REVERT: F 210 GLU cc_start: 0.6727 (tt0) cc_final: 0.6153 (tt0) REVERT: G 5 GLN cc_start: 0.5238 (OUTLIER) cc_final: 0.4829 (pm20) REVERT: G 23 GLN cc_start: 0.8246 (tp-100) cc_final: 0.7747 (tp40) REVERT: G 33 ARG cc_start: 0.7417 (ptp-170) cc_final: 0.7145 (mtm180) REVERT: G 89 ILE cc_start: 0.9312 (mm) cc_final: 0.8961 (mm) REVERT: G 104 ASP cc_start: 0.6705 (t70) cc_final: 0.6201 (t0) REVERT: G 171 VAL cc_start: 0.7104 (t) cc_final: 0.6240 (p) REVERT: 1 72 ILE cc_start: 0.8922 (mm) cc_final: 0.8719 (mm) REVERT: 1 173 TYR cc_start: 0.5846 (t80) cc_final: 0.5271 (t80) REVERT: 2 19 CYS cc_start: 0.5449 (m) cc_final: 0.5102 (m) REVERT: 2 48 ILE cc_start: 0.8321 (mm) cc_final: 0.8066 (mm) REVERT: 2 81 ARG cc_start: 0.8540 (mmt90) cc_final: 0.8281 (mmt90) REVERT: 2 125 ILE cc_start: 0.8364 (mp) cc_final: 0.8134 (mp) REVERT: 2 172 ILE cc_start: 0.7121 (tp) cc_final: 0.6876 (tp) REVERT: 2 188 VAL cc_start: 0.7051 (p) cc_final: 0.6781 (p) REVERT: 2 197 TYR cc_start: 0.4418 (t80) cc_final: 0.4016 (t80) REVERT: 3 46 TYR cc_start: 0.7256 (m-80) cc_final: 0.6828 (m-10) REVERT: 4 48 ILE cc_start: 0.9110 (mm) cc_final: 0.8375 (mm) REVERT: 4 87 VAL cc_start: 0.8521 (t) cc_final: 0.8191 (t) REVERT: 4 123 TYR cc_start: 0.8597 (m-80) cc_final: 0.7952 (m-80) REVERT: 5 79 ILE cc_start: 0.8656 (mt) cc_final: 0.8353 (mt) REVERT: 5 132 ILE cc_start: 0.7421 (mt) cc_final: 0.7132 (mt) REVERT: 5 146 THR cc_start: 0.6489 (p) cc_final: 0.6206 (p) REVERT: 6 33 MET cc_start: 0.2058 (pmm) cc_final: 0.1852 (pmm) REVERT: 6 81 ARG cc_start: 0.7595 (ttm110) cc_final: 0.7296 (tpp80) REVERT: 6 137 ILE cc_start: 0.7480 (mm) cc_final: 0.7256 (mp) REVERT: 7 155 PHE cc_start: 0.7009 (t80) cc_final: 0.6573 (t80) outliers start: 8 outliers final: 0 residues processed: 1297 average time/residue: 0.3918 time to fit residues: 760.9773 Evaluate side-chains 1112 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1110 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 232 optimal weight: 2.9990 chunk 190 optimal weight: 0.2980 chunk 77 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 chunk 302 optimal weight: 0.5980 chunk 249 optimal weight: 0.8980 chunk 277 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 224 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN F 99 ASN G 5 GLN 3 75 ASN 5 109 GLN 6 96 ASN 6 198 GLN 7 75 ASN 7 96 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24968 Z= 0.280 Angle : 0.739 14.347 33660 Z= 0.402 Chirality : 0.048 0.202 3881 Planarity : 0.005 0.055 4329 Dihedral : 5.957 52.558 3498 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.04 % Favored : 95.64 % Rotamer: Outliers : 0.38 % Allowed : 2.71 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3122 helix: 0.22 (0.14), residues: 1216 sheet: 0.07 (0.19), residues: 618 loop : -1.63 (0.15), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 73 PHE 0.024 0.002 PHE D 185 TYR 0.031 0.002 TYR 6 46 ARG 0.014 0.001 ARG 4 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1255 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1245 time to evaluate : 2.875 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: A 69 LYS cc_start: 0.8585 (tttm) cc_final: 0.8211 (tttm) REVERT: A 94 ILE cc_start: 0.9274 (mt) cc_final: 0.8993 (mt) REVERT: A 111 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6295 (mm-30) REVERT: A 121 GLN cc_start: 0.8299 (tp40) cc_final: 0.7671 (tm-30) REVERT: A 166 MET cc_start: 0.7164 (mtp) cc_final: 0.6798 (ttt) REVERT: A 186 ASP cc_start: 0.6477 (p0) cc_final: 0.5977 (p0) REVERT: A 191 LEU cc_start: 0.7862 (tp) cc_final: 0.7620 (tp) REVERT: A 211 VAL cc_start: 0.8535 (t) cc_final: 0.7296 (p) REVERT: A 223 GLU cc_start: 0.6603 (tt0) cc_final: 0.5824 (tt0) REVERT: B 18 ASP cc_start: 0.6682 (m-30) cc_final: 0.6290 (m-30) REVERT: B 38 ILE cc_start: 0.8404 (mt) cc_final: 0.7973 (mt) REVERT: B 98 ILE cc_start: 0.9028 (mm) cc_final: 0.8761 (mm) REVERT: B 151 ASP cc_start: 0.8382 (t0) cc_final: 0.8124 (t0) REVERT: B 152 PRO cc_start: 0.9556 (Cg_exo) cc_final: 0.9077 (Cg_endo) REVERT: B 181 ASP cc_start: 0.7131 (m-30) cc_final: 0.6879 (m-30) REVERT: B 186 ASP cc_start: 0.6803 (p0) cc_final: 0.6441 (p0) REVERT: B 196 MET cc_start: 0.6982 (mmm) cc_final: 0.6718 (mmm) REVERT: B 201 GLU cc_start: 0.5426 (tm-30) cc_final: 0.5153 (tm-30) REVERT: B 208 ASN cc_start: 0.6647 (p0) cc_final: 0.6261 (p0) REVERT: B 229 LEU cc_start: 0.7851 (mt) cc_final: 0.7587 (mt) REVERT: B 238 GLU cc_start: 0.5371 (mt-10) cc_final: 0.4915 (mt-10) REVERT: C 26 TYR cc_start: 0.8298 (m-10) cc_final: 0.7996 (m-10) REVERT: C 52 LYS cc_start: 0.7657 (tttt) cc_final: 0.6319 (tttt) REVERT: C 123 TYR cc_start: 0.7765 (m-80) cc_final: 0.5880 (m-80) REVERT: C 137 LEU cc_start: 0.8664 (mt) cc_final: 0.8082 (mt) REVERT: C 202 SER cc_start: 0.7978 (p) cc_final: 0.7775 (p) REVERT: C 208 ASN cc_start: 0.7449 (p0) cc_final: 0.7011 (p0) REVERT: C 214 VAL cc_start: 0.8509 (t) cc_final: 0.8191 (t) REVERT: C 225 SER cc_start: 0.7068 (p) cc_final: 0.2777 (p) REVERT: D 64 ILE cc_start: 0.7131 (pt) cc_final: 0.6864 (pt) REVERT: D 95 GLU cc_start: 0.7381 (tt0) cc_final: 0.7167 (tt0) REVERT: D 174 PHE cc_start: 0.7116 (t80) cc_final: 0.6349 (t80) REVERT: D 178 GLU cc_start: 0.6450 (mt-10) cc_final: 0.6215 (mt-10) REVERT: D 239 ARG cc_start: 0.5858 (mtp-110) cc_final: 0.5473 (mtp180) REVERT: D 240 ILE cc_start: 0.7616 (pt) cc_final: 0.6934 (pt) REVERT: E 8 TYR cc_start: 0.7563 (m-10) cc_final: 0.6749 (m-80) REVERT: E 25 GLU cc_start: 0.6576 (tp30) cc_final: 0.5768 (tp30) REVERT: E 185 PHE cc_start: 0.8069 (t80) cc_final: 0.7783 (t80) REVERT: E 186 ASP cc_start: 0.6286 (m-30) cc_final: 0.5991 (m-30) REVERT: E 189 MET cc_start: 0.6984 (tmm) cc_final: 0.6673 (ttp) REVERT: E 191 LEU cc_start: 0.8498 (tp) cc_final: 0.8253 (tp) REVERT: E 218 ASP cc_start: 0.8436 (p0) cc_final: 0.7570 (p0) REVERT: F 9 ASP cc_start: 0.8558 (p0) cc_final: 0.7878 (p0) REVERT: F 26 TYR cc_start: 0.8652 (m-10) cc_final: 0.8220 (m-10) REVERT: F 88 LEU cc_start: 0.9131 (tp) cc_final: 0.8894 (tp) REVERT: F 99 ASN cc_start: 0.8203 (t0) cc_final: 0.7990 (t0) REVERT: F 120 LYS cc_start: 0.8431 (mtmm) cc_final: 0.7734 (ttmm) REVERT: F 150 THR cc_start: 0.7619 (p) cc_final: 0.7263 (p) REVERT: G 5 GLN cc_start: 0.5642 (OUTLIER) cc_final: 0.4845 (pt0) REVERT: G 47 ILE cc_start: 0.8644 (mt) cc_final: 0.8344 (mt) REVERT: G 73 HIS cc_start: 0.7027 (p-80) cc_final: 0.6659 (p-80) REVERT: G 143 GLU cc_start: 0.6205 (pm20) cc_final: 0.5653 (pm20) REVERT: G 191 LEU cc_start: 0.7628 (tp) cc_final: 0.6973 (tp) REVERT: G 211 VAL cc_start: 0.9066 (t) cc_final: 0.8790 (t) REVERT: G 234 GLU cc_start: 0.6348 (pp20) cc_final: 0.6058 (pp20) REVERT: G 237 ASN cc_start: 0.4541 (m110) cc_final: 0.3563 (m110) REVERT: 1 87 VAL cc_start: 0.8638 (t) cc_final: 0.8331 (p) REVERT: 1 173 TYR cc_start: 0.5934 (t80) cc_final: 0.5352 (t80) REVERT: 1 190 LYS cc_start: 0.8387 (ptpp) cc_final: 0.8081 (ptmt) REVERT: 1 208 LEU cc_start: 0.3883 (pp) cc_final: 0.3522 (pp) REVERT: 2 188 VAL cc_start: 0.7290 (p) cc_final: 0.7069 (p) REVERT: 2 197 TYR cc_start: 0.4557 (t80) cc_final: 0.4247 (t80) REVERT: 3 46 TYR cc_start: 0.7577 (m-80) cc_final: 0.6792 (m-80) REVERT: 3 48 ILE cc_start: 0.8930 (tp) cc_final: 0.8645 (tp) REVERT: 4 48 ILE cc_start: 0.9268 (mm) cc_final: 0.8863 (mm) REVERT: 4 88 ARG cc_start: 0.7321 (ttp-170) cc_final: 0.7105 (ttp-170) REVERT: 4 123 TYR cc_start: 0.8447 (m-80) cc_final: 0.7746 (m-80) REVERT: 4 144 SER cc_start: 0.7273 (p) cc_final: 0.6920 (p) REVERT: 5 33 MET cc_start: 0.1882 (mtt) cc_final: 0.0809 (ttm) REVERT: 6 46 TYR cc_start: 0.7219 (m-10) cc_final: 0.6926 (m-10) REVERT: 6 68 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7509 (ttp-110) REVERT: 6 79 ILE cc_start: 0.8839 (mt) cc_final: 0.8502 (mt) REVERT: 6 81 ARG cc_start: 0.7675 (ttm110) cc_final: 0.7415 (tpp80) REVERT: 6 195 GLU cc_start: 0.4478 (pt0) cc_final: 0.4207 (pt0) REVERT: 7 75 ASN cc_start: 0.7819 (m-40) cc_final: 0.7316 (m-40) REVERT: 7 79 ILE cc_start: 0.8789 (mt) cc_final: 0.8448 (mm) REVERT: 7 155 PHE cc_start: 0.7108 (t80) cc_final: 0.6880 (t80) REVERT: 7 162 ASP cc_start: 0.5852 (p0) cc_final: 0.5467 (p0) outliers start: 10 outliers final: 2 residues processed: 1251 average time/residue: 0.3666 time to fit residues: 700.8736 Evaluate side-chains 1113 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1110 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 1.9990 chunk 210 optimal weight: 0.5980 chunk 145 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 297 optimal weight: 2.9990 chunk 146 optimal weight: 0.4980 chunk 266 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN G 5 GLN 3 75 ASN 4 75 ASN 4 96 ASN 6 75 ASN 7 75 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.6399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24968 Z= 0.283 Angle : 0.720 14.467 33660 Z= 0.389 Chirality : 0.048 0.202 3881 Planarity : 0.005 0.054 4329 Dihedral : 5.781 49.820 3498 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.88 % Favored : 95.80 % Rotamer: Outliers : 0.19 % Allowed : 3.78 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: -0.71 (0.14), residues: 3122 helix: 0.30 (0.15), residues: 1211 sheet: 0.12 (0.19), residues: 623 loop : -1.49 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 73 PHE 0.019 0.002 PHE 7 65 TYR 0.048 0.002 TYR C 123 ARG 0.013 0.001 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1247 time to evaluate : 2.676 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: A 111 GLU cc_start: 0.6665 (mm-30) cc_final: 0.6334 (mm-30) REVERT: A 186 ASP cc_start: 0.6681 (p0) cc_final: 0.6149 (p0) REVERT: A 191 LEU cc_start: 0.7741 (tp) cc_final: 0.7521 (tp) REVERT: A 196 MET cc_start: 0.7448 (mmm) cc_final: 0.6726 (mmm) REVERT: A 208 ASN cc_start: 0.7702 (p0) cc_final: 0.7227 (p0) REVERT: A 211 VAL cc_start: 0.8728 (t) cc_final: 0.7456 (p) REVERT: A 223 GLU cc_start: 0.6864 (tt0) cc_final: 0.6641 (tt0) REVERT: B 31 VAL cc_start: 0.9192 (t) cc_final: 0.8951 (t) REVERT: B 38 ILE cc_start: 0.8349 (mt) cc_final: 0.7820 (mt) REVERT: B 93 ARG cc_start: 0.8151 (mtt-85) cc_final: 0.7889 (mtt-85) REVERT: B 95 GLU cc_start: 0.8052 (tp30) cc_final: 0.7702 (tp30) REVERT: B 104 ASP cc_start: 0.7335 (t0) cc_final: 0.7096 (t0) REVERT: B 151 ASP cc_start: 0.8494 (t0) cc_final: 0.8223 (t0) REVERT: B 152 PRO cc_start: 0.9634 (Cg_exo) cc_final: 0.9301 (Cg_endo) REVERT: B 186 ASP cc_start: 0.7189 (p0) cc_final: 0.6956 (p0) REVERT: B 201 GLU cc_start: 0.5649 (tm-30) cc_final: 0.5151 (tm-30) REVERT: B 208 ASN cc_start: 0.6873 (p0) cc_final: 0.6534 (p0) REVERT: B 229 LEU cc_start: 0.8066 (mt) cc_final: 0.7787 (mt) REVERT: B 238 GLU cc_start: 0.5464 (mt-10) cc_final: 0.4967 (mt-10) REVERT: B 243 LEU cc_start: 0.7281 (mp) cc_final: 0.7058 (mt) REVERT: C 26 TYR cc_start: 0.8480 (m-10) cc_final: 0.7958 (m-10) REVERT: C 41 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8441 (tttt) REVERT: C 171 VAL cc_start: 0.8211 (t) cc_final: 0.8003 (t) REVERT: C 182 ASP cc_start: 0.6066 (p0) cc_final: 0.5325 (p0) REVERT: C 202 SER cc_start: 0.8525 (p) cc_final: 0.8268 (p) REVERT: C 217 ASP cc_start: 0.6916 (p0) cc_final: 0.6641 (p0) REVERT: D 38 ILE cc_start: 0.8750 (mt) cc_final: 0.8521 (mt) REVERT: D 60 GLU cc_start: 0.6928 (pp20) cc_final: 0.5629 (pm20) REVERT: D 64 ILE cc_start: 0.7221 (pt) cc_final: 0.6960 (pt) REVERT: D 91 ARG cc_start: 0.8485 (tpt90) cc_final: 0.8226 (tpt170) REVERT: D 116 ILE cc_start: 0.9004 (tp) cc_final: 0.8788 (tp) REVERT: D 240 ILE cc_start: 0.7640 (pt) cc_final: 0.7309 (pt) REVERT: E 8 TYR cc_start: 0.7724 (m-10) cc_final: 0.6965 (m-80) REVERT: E 25 GLU cc_start: 0.6571 (tp30) cc_final: 0.5854 (tp30) REVERT: E 185 PHE cc_start: 0.8139 (t80) cc_final: 0.7858 (t80) REVERT: E 186 ASP cc_start: 0.6193 (m-30) cc_final: 0.5984 (m-30) REVERT: E 200 ILE cc_start: 0.8363 (pt) cc_final: 0.8149 (pt) REVERT: E 218 ASP cc_start: 0.8268 (p0) cc_final: 0.7471 (p0) REVERT: F 9 ASP cc_start: 0.8572 (p0) cc_final: 0.7950 (p0) REVERT: F 26 TYR cc_start: 0.8628 (m-10) cc_final: 0.8143 (m-10) REVERT: F 84 ASP cc_start: 0.7366 (m-30) cc_final: 0.7107 (m-30) REVERT: F 99 ASN cc_start: 0.8250 (t0) cc_final: 0.7995 (t0) REVERT: F 103 TYR cc_start: 0.8886 (m-80) cc_final: 0.8657 (m-80) REVERT: F 150 THR cc_start: 0.7809 (p) cc_final: 0.7566 (p) REVERT: F 228 GLU cc_start: 0.6259 (tp30) cc_final: 0.6039 (tp30) REVERT: F 232 TYR cc_start: 0.6928 (m-80) cc_final: 0.6604 (m-10) REVERT: G 5 GLN cc_start: 0.5662 (OUTLIER) cc_final: 0.4972 (pt0) REVERT: G 47 ILE cc_start: 0.8554 (mt) cc_final: 0.8321 (mt) REVERT: G 73 HIS cc_start: 0.7355 (p-80) cc_final: 0.6813 (p-80) REVERT: G 104 ASP cc_start: 0.6583 (t70) cc_final: 0.6297 (t0) REVERT: G 148 TYR cc_start: 0.8713 (m-80) cc_final: 0.8373 (m-10) REVERT: G 172 THR cc_start: 0.6612 (m) cc_final: 0.6110 (m) REVERT: G 191 LEU cc_start: 0.7651 (tp) cc_final: 0.7308 (tp) REVERT: G 209 ILE cc_start: 0.8647 (pt) cc_final: 0.8428 (pt) REVERT: G 234 GLU cc_start: 0.6713 (pp20) cc_final: 0.6195 (pp20) REVERT: 1 52 MET cc_start: 0.6545 (ttm) cc_final: 0.6322 (ttp) REVERT: 1 87 VAL cc_start: 0.8731 (t) cc_final: 0.8419 (p) REVERT: 1 122 ILE cc_start: 0.7553 (mm) cc_final: 0.7298 (mm) REVERT: 1 173 TYR cc_start: 0.5896 (t80) cc_final: 0.5337 (t80) REVERT: 1 190 LYS cc_start: 0.8466 (ptpp) cc_final: 0.8218 (ptmm) REVERT: 1 208 LEU cc_start: 0.3492 (pp) cc_final: 0.3053 (pp) REVERT: 2 48 ILE cc_start: 0.8423 (mm) cc_final: 0.8197 (mm) REVERT: 2 116 ASP cc_start: 0.5270 (p0) cc_final: 0.4957 (p0) REVERT: 3 46 TYR cc_start: 0.7299 (m-80) cc_final: 0.6606 (m-80) REVERT: 3 87 VAL cc_start: 0.8365 (t) cc_final: 0.7976 (t) REVERT: 4 48 ILE cc_start: 0.9209 (mm) cc_final: 0.8572 (mm) REVERT: 4 75 ASN cc_start: 0.8135 (m110) cc_final: 0.7783 (m-40) REVERT: 4 144 SER cc_start: 0.7396 (p) cc_final: 0.7079 (p) REVERT: 4 151 LEU cc_start: 0.6410 (tp) cc_final: 0.6140 (tp) REVERT: 5 33 MET cc_start: 0.1958 (mtt) cc_final: 0.0985 (ttm) REVERT: 5 46 TYR cc_start: 0.7963 (m-80) cc_final: 0.7520 (m-10) REVERT: 5 146 THR cc_start: 0.6499 (p) cc_final: 0.6290 (p) REVERT: 6 79 ILE cc_start: 0.8672 (mt) cc_final: 0.8360 (mt) REVERT: 6 90 ILE cc_start: 0.8818 (mm) cc_final: 0.8442 (mm) REVERT: 7 116 ASP cc_start: 0.7066 (p0) cc_final: 0.6805 (p0) REVERT: 7 162 ASP cc_start: 0.6184 (p0) cc_final: 0.5771 (p0) outliers start: 5 outliers final: 0 residues processed: 1250 average time/residue: 0.3640 time to fit residues: 699.7043 Evaluate side-chains 1138 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1137 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 254 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 267 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN G 5 GLN 2 96 ASN 2 198 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 24968 Z= 0.292 Angle : 0.713 14.420 33660 Z= 0.383 Chirality : 0.048 0.189 3881 Planarity : 0.004 0.048 4329 Dihedral : 5.671 50.672 3498 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.04 % Favored : 95.71 % Rotamer: Outliers : 0.15 % Allowed : 2.45 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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 (0.14), residues: 3122 helix: 0.30 (0.15), residues: 1211 sheet: -0.01 (0.19), residues: 626 loop : -1.38 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 73 PHE 0.020 0.002 PHE C 132 TYR 0.031 0.002 TYR 7 148 ARG 0.009 0.001 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1232 time to evaluate : 2.482 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: A 84 ASP cc_start: 0.6180 (m-30) cc_final: 0.5764 (m-30) REVERT: A 111 GLU cc_start: 0.6476 (mm-30) cc_final: 0.6048 (mm-30) REVERT: A 186 ASP cc_start: 0.6755 (p0) cc_final: 0.6107 (p0) REVERT: A 196 MET cc_start: 0.7594 (mmm) cc_final: 0.7195 (tpp) REVERT: A 208 ASN cc_start: 0.7714 (p0) cc_final: 0.7109 (p0) REVERT: A 211 VAL cc_start: 0.8677 (t) cc_final: 0.7429 (p) REVERT: B 9 ASP cc_start: 0.7081 (p0) cc_final: 0.6546 (p0) REVERT: B 36 THR cc_start: 0.8313 (m) cc_final: 0.8039 (m) REVERT: B 93 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7876 (mtt-85) REVERT: B 95 GLU cc_start: 0.8063 (tp30) cc_final: 0.7765 (tp30) REVERT: B 104 ASP cc_start: 0.7184 (t0) cc_final: 0.6977 (t0) REVERT: B 121 GLN cc_start: 0.7849 (tp-100) cc_final: 0.7572 (tp-100) REVERT: B 151 ASP cc_start: 0.8670 (t0) cc_final: 0.8399 (t0) REVERT: B 152 PRO cc_start: 0.9675 (Cg_exo) cc_final: 0.9315 (Cg_endo) REVERT: B 186 ASP cc_start: 0.7274 (p0) cc_final: 0.6994 (p0) REVERT: B 196 MET cc_start: 0.7291 (mmt) cc_final: 0.6799 (mmm) REVERT: B 201 GLU cc_start: 0.5782 (tm-30) cc_final: 0.5335 (tm-30) REVERT: B 208 ASN cc_start: 0.7007 (p0) cc_final: 0.6768 (p0) REVERT: B 224 VAL cc_start: 0.7759 (p) cc_final: 0.7349 (p) REVERT: B 229 LEU cc_start: 0.7918 (mt) cc_final: 0.7659 (mt) REVERT: B 238 GLU cc_start: 0.5307 (mt-10) cc_final: 0.5066 (mt-10) REVERT: B 242 GLU cc_start: 0.6869 (pm20) cc_final: 0.6627 (pm20) REVERT: C 26 TYR cc_start: 0.8542 (m-10) cc_final: 0.8095 (m-10) REVERT: C 89 ILE cc_start: 0.8240 (pt) cc_final: 0.7982 (pt) REVERT: C 182 ASP cc_start: 0.6015 (p0) cc_final: 0.5361 (p0) REVERT: C 214 VAL cc_start: 0.8547 (t) cc_final: 0.8309 (t) REVERT: C 217 ASP cc_start: 0.7003 (p0) cc_final: 0.6712 (p0) REVERT: D 60 GLU cc_start: 0.6776 (pp20) cc_final: 0.5438 (pm20) REVERT: D 64 ILE cc_start: 0.7364 (pt) cc_final: 0.7152 (pt) REVERT: D 91 ARG cc_start: 0.8509 (tpt90) cc_final: 0.8108 (tpt170) REVERT: D 108 THR cc_start: 0.8902 (p) cc_final: 0.8655 (m) REVERT: D 240 ILE cc_start: 0.7689 (pt) cc_final: 0.7151 (pt) REVERT: E 8 TYR cc_start: 0.7760 (m-10) cc_final: 0.7039 (m-80) REVERT: E 25 GLU cc_start: 0.6567 (tp30) cc_final: 0.5993 (tp30) REVERT: E 185 PHE cc_start: 0.8060 (t80) cc_final: 0.7738 (t80) REVERT: E 200 ILE cc_start: 0.8425 (pt) cc_final: 0.8152 (pt) REVERT: E 218 ASP cc_start: 0.8396 (p0) cc_final: 0.7631 (p0) REVERT: F 9 ASP cc_start: 0.8655 (p0) cc_final: 0.8101 (p0) REVERT: F 15 PHE cc_start: 0.8657 (m-80) cc_final: 0.8433 (m-80) REVERT: F 26 TYR cc_start: 0.8624 (m-10) cc_final: 0.8205 (m-10) REVERT: F 150 THR cc_start: 0.7972 (p) cc_final: 0.7766 (p) REVERT: F 215 LYS cc_start: 0.6092 (mtpp) cc_final: 0.5669 (tptm) REVERT: F 232 TYR cc_start: 0.6926 (m-80) cc_final: 0.6721 (m-10) REVERT: G 5 GLN cc_start: 0.5802 (OUTLIER) cc_final: 0.5093 (pt0) REVERT: G 47 ILE cc_start: 0.8682 (mt) cc_final: 0.8343 (mt) REVERT: G 66 LYS cc_start: 0.8494 (tptt) cc_final: 0.8153 (mptt) REVERT: G 71 ASP cc_start: 0.6140 (m-30) cc_final: 0.5937 (m-30) REVERT: G 73 HIS cc_start: 0.7413 (p-80) cc_final: 0.6609 (p90) REVERT: G 191 LEU cc_start: 0.7827 (tp) cc_final: 0.7596 (tp) REVERT: G 211 VAL cc_start: 0.9234 (t) cc_final: 0.9027 (t) REVERT: G 234 GLU cc_start: 0.6571 (pp20) cc_final: 0.6129 (pp20) REVERT: 1 173 TYR cc_start: 0.6053 (t80) cc_final: 0.5324 (t80) REVERT: 1 190 LYS cc_start: 0.8433 (ptpp) cc_final: 0.8200 (ptmm) REVERT: 1 208 LEU cc_start: 0.4840 (pp) cc_final: 0.4603 (pp) REVERT: 2 48 ILE cc_start: 0.8380 (mm) cc_final: 0.7999 (mm) REVERT: 2 52 MET cc_start: 0.6170 (ttm) cc_final: 0.5790 (ttt) REVERT: 2 116 ASP cc_start: 0.5789 (p0) cc_final: 0.5299 (p0) REVERT: 3 46 TYR cc_start: 0.7419 (m-80) cc_final: 0.6796 (m-80) REVERT: 3 48 ILE cc_start: 0.8697 (tp) cc_final: 0.8398 (tp) REVERT: 4 48 ILE cc_start: 0.9186 (mm) cc_final: 0.8865 (mm) REVERT: 4 123 TYR cc_start: 0.8749 (m-80) cc_final: 0.8385 (m-80) REVERT: 5 46 TYR cc_start: 0.7830 (m-80) cc_final: 0.7123 (m-10) REVERT: 5 146 THR cc_start: 0.6843 (p) cc_final: 0.6500 (p) REVERT: 6 25 MET cc_start: 0.4507 (mtp) cc_final: 0.4185 (mtp) REVERT: 6 68 ARG cc_start: 0.7987 (ttp-110) cc_final: 0.7675 (ttp-110) REVERT: 6 120 LYS cc_start: 0.6554 (mtmt) cc_final: 0.6125 (mttm) REVERT: 7 116 ASP cc_start: 0.7057 (p0) cc_final: 0.6774 (p0) outliers start: 4 outliers final: 0 residues processed: 1235 average time/residue: 0.3573 time to fit residues: 683.5317 Evaluate side-chains 1123 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1122 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 0.9980 chunk 268 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 174 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 298 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 156 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 5 GLN 2 96 ASN 2 198 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.7126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24968 Z= 0.254 Angle : 0.698 14.086 33660 Z= 0.375 Chirality : 0.048 0.264 3881 Planarity : 0.004 0.080 4329 Dihedral : 5.581 42.299 3498 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.00 % Favored : 95.77 % Rotamer: Outliers : 0.08 % Allowed : 1.64 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: -0.65 (0.14), residues: 3122 helix: 0.31 (0.15), residues: 1206 sheet: 0.02 (0.19), residues: 619 loop : -1.31 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 73 PHE 0.020 0.002 PHE 1 196 TYR 0.032 0.002 TYR 2 46 ARG 0.012 0.001 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1224 time to evaluate : 2.760 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: A 36 THR cc_start: 0.8861 (m) cc_final: 0.8359 (p) REVERT: A 84 ASP cc_start: 0.6118 (m-30) cc_final: 0.5847 (m-30) REVERT: A 181 ASP cc_start: 0.6064 (m-30) cc_final: 0.5810 (m-30) REVERT: A 186 ASP cc_start: 0.6574 (p0) cc_final: 0.5973 (p0) REVERT: A 196 MET cc_start: 0.7727 (mmm) cc_final: 0.7289 (tpp) REVERT: A 208 ASN cc_start: 0.7578 (p0) cc_final: 0.7303 (p0) REVERT: A 211 VAL cc_start: 0.8419 (t) cc_final: 0.7544 (p) REVERT: B 8 TYR cc_start: 0.7942 (m-80) cc_final: 0.7732 (m-80) REVERT: B 36 THR cc_start: 0.8458 (m) cc_final: 0.8184 (m) REVERT: B 58 LEU cc_start: 0.7978 (mt) cc_final: 0.7763 (mt) REVERT: B 104 ASP cc_start: 0.7206 (t0) cc_final: 0.6936 (t0) REVERT: B 152 PRO cc_start: 0.9653 (Cg_exo) cc_final: 0.9342 (Cg_endo) REVERT: B 196 MET cc_start: 0.7102 (mmt) cc_final: 0.6673 (mmm) REVERT: B 201 GLU cc_start: 0.5821 (tm-30) cc_final: 0.5568 (tm-30) REVERT: B 208 ASN cc_start: 0.7020 (p0) cc_final: 0.6773 (p0) REVERT: B 238 GLU cc_start: 0.5473 (mt-10) cc_final: 0.5171 (mt-10) REVERT: B 239 ARG cc_start: 0.5191 (ttp-170) cc_final: 0.4890 (ttp-170) REVERT: C 52 LYS cc_start: 0.7420 (tttt) cc_final: 0.7200 (tttt) REVERT: C 182 ASP cc_start: 0.6300 (p0) cc_final: 0.5617 (p0) REVERT: C 202 SER cc_start: 0.8463 (p) cc_final: 0.8163 (p) REVERT: C 214 VAL cc_start: 0.8452 (t) cc_final: 0.8225 (t) REVERT: C 217 ASP cc_start: 0.7121 (p0) cc_final: 0.6832 (p0) REVERT: C 225 SER cc_start: 0.6494 (t) cc_final: 0.5992 (t) REVERT: D 91 ARG cc_start: 0.8501 (tpt90) cc_final: 0.8066 (tpt170) REVERT: D 228 GLU cc_start: 0.5747 (tp30) cc_final: 0.5499 (tp30) REVERT: E 8 TYR cc_start: 0.7687 (m-10) cc_final: 0.6926 (m-80) REVERT: E 25 GLU cc_start: 0.6551 (tp30) cc_final: 0.5961 (tp30) REVERT: E 185 PHE cc_start: 0.8109 (t80) cc_final: 0.7763 (t80) REVERT: E 218 ASP cc_start: 0.8308 (p0) cc_final: 0.7789 (p0) REVERT: F 9 ASP cc_start: 0.8273 (p0) cc_final: 0.7556 (p0) REVERT: F 26 TYR cc_start: 0.8597 (m-10) cc_final: 0.8191 (m-10) REVERT: F 52 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8455 (mtpp) REVERT: F 112 LEU cc_start: 0.9167 (tp) cc_final: 0.8960 (tp) REVERT: F 232 TYR cc_start: 0.6924 (m-80) cc_final: 0.6708 (m-10) REVERT: G 5 GLN cc_start: 0.5891 (OUTLIER) cc_final: 0.4996 (pt0) REVERT: G 73 HIS cc_start: 0.7180 (p-80) cc_final: 0.6234 (p90) REVERT: G 112 LEU cc_start: 0.8798 (tp) cc_final: 0.8535 (tp) REVERT: G 191 LEU cc_start: 0.7834 (tp) cc_final: 0.7495 (tp) REVERT: G 196 MET cc_start: 0.6749 (tpp) cc_final: 0.6492 (tpp) REVERT: G 209 ILE cc_start: 0.8653 (pt) cc_final: 0.8404 (pt) REVERT: G 234 GLU cc_start: 0.6410 (pp20) cc_final: 0.5612 (pp20) REVERT: 1 172 ILE cc_start: 0.6239 (mm) cc_final: 0.5126 (mm) REVERT: 1 173 TYR cc_start: 0.6006 (t80) cc_final: 0.5238 (t80) REVERT: 1 190 LYS cc_start: 0.8096 (ptpp) cc_final: 0.7878 (ptmm) REVERT: 1 193 GLU cc_start: 0.6316 (tm-30) cc_final: 0.6018 (tm-30) REVERT: 1 208 LEU cc_start: 0.4696 (pp) cc_final: 0.4481 (pp) REVERT: 2 45 ILE cc_start: 0.7284 (tt) cc_final: 0.6917 (tt) REVERT: 2 48 ILE cc_start: 0.8405 (mm) cc_final: 0.8061 (mm) REVERT: 2 52 MET cc_start: 0.6241 (ttm) cc_final: 0.5824 (ttt) REVERT: 2 86 THR cc_start: 0.8486 (t) cc_final: 0.7615 (t) REVERT: 2 116 ASP cc_start: 0.5923 (p0) cc_final: 0.5217 (p0) REVERT: 3 46 TYR cc_start: 0.7320 (m-80) cc_final: 0.6779 (m-80) REVERT: 4 48 ILE cc_start: 0.9237 (mm) cc_final: 0.8857 (mm) REVERT: 4 52 MET cc_start: 0.6889 (ttm) cc_final: 0.6566 (ttp) REVERT: 4 123 TYR cc_start: 0.8777 (m-80) cc_final: 0.8251 (m-80) REVERT: 5 46 TYR cc_start: 0.7860 (m-80) cc_final: 0.7250 (m-10) REVERT: 5 120 LYS cc_start: 0.7254 (mtmm) cc_final: 0.6913 (mttp) REVERT: 5 146 THR cc_start: 0.6897 (p) cc_final: 0.6586 (p) REVERT: 6 90 ILE cc_start: 0.8877 (mm) cc_final: 0.8530 (mm) REVERT: 6 120 LYS cc_start: 0.6428 (mtmt) cc_final: 0.6188 (mttp) REVERT: 7 116 ASP cc_start: 0.7021 (p0) cc_final: 0.6773 (p0) REVERT: 7 134 GLU cc_start: 0.7495 (mp0) cc_final: 0.6162 (mp0) REVERT: H 396 MET cc_start: 0.6709 (ptp) cc_final: 0.6453 (ptp) outliers start: 2 outliers final: 0 residues processed: 1225 average time/residue: 0.3673 time to fit residues: 696.9411 Evaluate side-chains 1130 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1129 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 217 optimal weight: 0.0670 chunk 168 optimal weight: 0.9990 chunk 250 optimal weight: 1.9990 chunk 166 optimal weight: 0.4980 chunk 296 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 5 GLN ** 1 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 198 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 75 ASN ** 5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.7372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24968 Z= 0.263 Angle : 0.706 14.048 33660 Z= 0.377 Chirality : 0.048 0.198 3881 Planarity : 0.004 0.060 4329 Dihedral : 5.528 42.336 3498 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.04 % Favored : 95.74 % Rotamer: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: -0.63 (0.14), residues: 3122 helix: 0.33 (0.15), residues: 1210 sheet: 0.02 (0.19), residues: 615 loop : -1.30 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 73 PHE 0.023 0.002 PHE A 119 TYR 0.040 0.002 TYR 4 148 ARG 0.010 0.001 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1208 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1207 time to evaluate : 2.806 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: A 36 THR cc_start: 0.8842 (m) cc_final: 0.8406 (p) REVERT: A 98 ILE cc_start: 0.8529 (mt) cc_final: 0.8276 (mt) REVERT: A 121 GLN cc_start: 0.7938 (tp40) cc_final: 0.7615 (tp40) REVERT: A 186 ASP cc_start: 0.6150 (p0) cc_final: 0.5761 (p0) REVERT: A 208 ASN cc_start: 0.7617 (p0) cc_final: 0.6798 (p0) REVERT: A 211 VAL cc_start: 0.8577 (t) cc_final: 0.7602 (p) REVERT: B 36 THR cc_start: 0.8416 (m) cc_final: 0.8145 (m) REVERT: B 130 ARG cc_start: 0.8470 (pmt-80) cc_final: 0.8094 (ppt170) REVERT: B 151 ASP cc_start: 0.8992 (t0) cc_final: 0.8736 (t0) REVERT: B 152 PRO cc_start: 0.9706 (Cg_exo) cc_final: 0.9478 (Cg_endo) REVERT: B 196 MET cc_start: 0.7080 (mmt) cc_final: 0.6851 (mmm) REVERT: B 198 LEU cc_start: 0.7507 (mt) cc_final: 0.7217 (mt) REVERT: B 201 GLU cc_start: 0.5457 (tm-30) cc_final: 0.5123 (tm-30) REVERT: B 208 ASN cc_start: 0.7101 (p0) cc_final: 0.6768 (p0) REVERT: C 52 LYS cc_start: 0.7516 (tttt) cc_final: 0.7197 (tttt) REVERT: C 89 ILE cc_start: 0.8049 (pt) cc_final: 0.7666 (pt) REVERT: C 182 ASP cc_start: 0.6289 (p0) cc_final: 0.5642 (p0) REVERT: C 184 SER cc_start: 0.5852 (p) cc_final: 0.5135 (m) REVERT: C 200 ILE cc_start: 0.8429 (pt) cc_final: 0.7983 (mt) REVERT: C 202 SER cc_start: 0.8372 (p) cc_final: 0.7972 (p) REVERT: C 217 ASP cc_start: 0.7192 (p0) cc_final: 0.6815 (p0) REVERT: C 219 ARG cc_start: 0.7447 (mmt90) cc_final: 0.7084 (mtt-85) REVERT: D 57 LYS cc_start: 0.7504 (pttm) cc_final: 0.7086 (mppt) REVERT: D 91 ARG cc_start: 0.8413 (tpt90) cc_final: 0.8052 (tpt170) REVERT: D 240 ILE cc_start: 0.7644 (pt) cc_final: 0.7069 (pt) REVERT: E 8 TYR cc_start: 0.7688 (m-10) cc_final: 0.6865 (m-80) REVERT: E 25 GLU cc_start: 0.6543 (tp30) cc_final: 0.5968 (tp30) REVERT: E 185 PHE cc_start: 0.8209 (t80) cc_final: 0.7832 (t80) REVERT: E 186 ASP cc_start: 0.6303 (m-30) cc_final: 0.6097 (m-30) REVERT: E 200 ILE cc_start: 0.8441 (pt) cc_final: 0.8068 (pt) REVERT: E 218 ASP cc_start: 0.8441 (p0) cc_final: 0.7943 (p0) REVERT: F 9 ASP cc_start: 0.8367 (p0) cc_final: 0.7575 (p0) REVERT: F 26 TYR cc_start: 0.8616 (m-10) cc_final: 0.8316 (m-10) REVERT: F 52 LYS cc_start: 0.8873 (mtpp) cc_final: 0.8619 (mtpp) REVERT: F 185 PHE cc_start: 0.6758 (t80) cc_final: 0.6159 (t80) REVERT: F 200 ILE cc_start: 0.8757 (mm) cc_final: 0.8376 (mm) REVERT: F 232 TYR cc_start: 0.6976 (m-80) cc_final: 0.6755 (m-10) REVERT: G 5 GLN cc_start: 0.5903 (OUTLIER) cc_final: 0.4828 (pt0) REVERT: G 73 HIS cc_start: 0.7113 (p-80) cc_final: 0.6188 (p90) REVERT: G 191 LEU cc_start: 0.7686 (tp) cc_final: 0.7456 (tp) REVERT: G 196 MET cc_start: 0.6868 (tpp) cc_final: 0.6498 (tpp) REVERT: G 234 GLU cc_start: 0.6288 (pp20) cc_final: 0.5593 (pp20) REVERT: 1 68 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8170 (ttm-80) REVERT: 1 172 ILE cc_start: 0.6183 (mm) cc_final: 0.5115 (mm) REVERT: 1 173 TYR cc_start: 0.6098 (t80) cc_final: 0.5398 (t80) REVERT: 1 190 LYS cc_start: 0.8096 (ptpp) cc_final: 0.7677 (ptmm) REVERT: 1 193 GLU cc_start: 0.6310 (tm-30) cc_final: 0.6047 (tm-30) REVERT: 1 208 LEU cc_start: 0.4967 (pp) cc_final: 0.4657 (pp) REVERT: 2 45 ILE cc_start: 0.7166 (tt) cc_final: 0.6917 (tt) REVERT: 2 48 ILE cc_start: 0.8475 (mm) cc_final: 0.8127 (mm) REVERT: 2 52 MET cc_start: 0.6087 (ttm) cc_final: 0.5609 (ttt) REVERT: 2 86 THR cc_start: 0.8545 (t) cc_final: 0.7613 (t) REVERT: 2 116 ASP cc_start: 0.5975 (p0) cc_final: 0.5269 (p0) REVERT: 2 172 ILE cc_start: 0.6900 (tp) cc_final: 0.6681 (tp) REVERT: 3 46 TYR cc_start: 0.7316 (m-80) cc_final: 0.6830 (m-80) REVERT: 4 48 ILE cc_start: 0.9239 (mm) cc_final: 0.8941 (mm) REVERT: 4 80 ARG cc_start: 0.8608 (mtt-85) cc_final: 0.8283 (mtt-85) REVERT: 4 123 TYR cc_start: 0.8807 (m-80) cc_final: 0.7933 (m-80) REVERT: 4 191 ILE cc_start: 0.7936 (tp) cc_final: 0.7701 (tp) REVERT: 5 46 TYR cc_start: 0.7762 (m-80) cc_final: 0.7241 (m-10) REVERT: 5 94 THR cc_start: 0.7397 (m) cc_final: 0.6881 (m) REVERT: 5 146 THR cc_start: 0.6982 (p) cc_final: 0.6740 (p) REVERT: 6 81 ARG cc_start: 0.7544 (ttm110) cc_final: 0.7290 (mmt90) REVERT: 6 90 ILE cc_start: 0.8930 (mm) cc_final: 0.8543 (mm) REVERT: 7 116 ASP cc_start: 0.7085 (p0) cc_final: 0.6754 (p0) REVERT: 7 162 ASP cc_start: 0.6205 (p0) cc_final: 0.5923 (p0) outliers start: 1 outliers final: 0 residues processed: 1208 average time/residue: 0.3610 time to fit residues: 683.8097 Evaluate side-chains 1119 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1118 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 177 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 146 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 233 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 5 GLN 1 198 GLN 2 198 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 198 GLN 6 75 ASN 6 99 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.7614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24968 Z= 0.280 Angle : 0.723 14.042 33660 Z= 0.387 Chirality : 0.049 0.308 3881 Planarity : 0.004 0.053 4329 Dihedral : 5.581 41.897 3498 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.07 % Favored : 95.77 % Rotamer: Outliers : 0.04 % Allowed : 1.30 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: -0.68 (0.14), residues: 3122 helix: 0.24 (0.15), residues: 1225 sheet: 0.03 (0.19), residues: 609 loop : -1.30 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 73 PHE 0.022 0.002 PHE B 175 TYR 0.033 0.002 TYR 7 148 ARG 0.013 0.001 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1227 time to evaluate : 3.029 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: A 98 ILE cc_start: 0.8464 (mt) cc_final: 0.8210 (mt) REVERT: A 181 ASP cc_start: 0.5900 (m-30) cc_final: 0.5669 (m-30) REVERT: A 186 ASP cc_start: 0.6322 (p0) cc_final: 0.5809 (p0) REVERT: A 208 ASN cc_start: 0.7674 (p0) cc_final: 0.7210 (p0) REVERT: A 211 VAL cc_start: 0.8531 (t) cc_final: 0.7675 (p) REVERT: B 36 THR cc_start: 0.8462 (m) cc_final: 0.8243 (m) REVERT: B 93 ARG cc_start: 0.7968 (mtt-85) cc_final: 0.7759 (mtt-85) REVERT: B 151 ASP cc_start: 0.8925 (t0) cc_final: 0.8696 (t0) REVERT: B 152 PRO cc_start: 0.9711 (Cg_exo) cc_final: 0.9492 (Cg_endo) REVERT: B 196 MET cc_start: 0.7253 (mmt) cc_final: 0.6829 (mmm) REVERT: C 44 GLU cc_start: 0.7501 (pm20) cc_final: 0.6963 (pm20) REVERT: C 52 LYS cc_start: 0.7514 (tttt) cc_final: 0.7142 (tttt) REVERT: C 89 ILE cc_start: 0.8152 (pt) cc_final: 0.7850 (pt) REVERT: C 175 PHE cc_start: 0.7768 (m-80) cc_final: 0.7549 (m-80) REVERT: C 182 ASP cc_start: 0.6319 (p0) cc_final: 0.5653 (p0) REVERT: C 184 SER cc_start: 0.5670 (p) cc_final: 0.4998 (m) REVERT: C 200 ILE cc_start: 0.8299 (pt) cc_final: 0.7901 (mt) REVERT: C 202 SER cc_start: 0.8402 (p) cc_final: 0.7959 (p) REVERT: C 214 VAL cc_start: 0.8562 (t) cc_final: 0.8321 (t) REVERT: C 217 ASP cc_start: 0.7254 (p0) cc_final: 0.6895 (p0) REVERT: D 57 LYS cc_start: 0.7772 (pttm) cc_final: 0.7243 (mppt) REVERT: D 81 LEU cc_start: 0.8311 (mp) cc_final: 0.8097 (mp) REVERT: D 91 ARG cc_start: 0.8416 (tpt90) cc_final: 0.7853 (tpt170) REVERT: D 151 ASP cc_start: 0.7916 (t70) cc_final: 0.7634 (t0) REVERT: E 8 TYR cc_start: 0.7375 (m-10) cc_final: 0.6572 (m-80) REVERT: E 25 GLU cc_start: 0.6569 (tp30) cc_final: 0.5966 (tp30) REVERT: E 185 PHE cc_start: 0.8161 (t80) cc_final: 0.7724 (t80) REVERT: E 186 ASP cc_start: 0.6276 (m-30) cc_final: 0.6009 (m-30) REVERT: E 200 ILE cc_start: 0.8532 (pt) cc_final: 0.8081 (pt) REVERT: E 218 ASP cc_start: 0.8421 (p0) cc_final: 0.7890 (p0) REVERT: F 9 ASP cc_start: 0.8296 (p0) cc_final: 0.7387 (p0) REVERT: F 95 GLU cc_start: 0.7457 (tp30) cc_final: 0.7080 (tp30) REVERT: F 147 LEU cc_start: 0.9057 (tp) cc_final: 0.8844 (tt) REVERT: F 160 LYS cc_start: 0.7525 (mtmt) cc_final: 0.7092 (mtpt) REVERT: F 177 LYS cc_start: 0.8188 (ptmm) cc_final: 0.7802 (ptmm) REVERT: F 181 ASP cc_start: 0.8080 (t0) cc_final: 0.7823 (t0) REVERT: G 5 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.5125 (pt0) REVERT: G 73 HIS cc_start: 0.7015 (p-80) cc_final: 0.6671 (p90) REVERT: G 191 LEU cc_start: 0.7581 (tp) cc_final: 0.7244 (tp) REVERT: G 196 MET cc_start: 0.6831 (tpp) cc_final: 0.6451 (tpp) REVERT: G 242 GLU cc_start: 0.7234 (pt0) cc_final: 0.6131 (tt0) REVERT: 1 68 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.8183 (ttm-80) REVERT: 1 172 ILE cc_start: 0.6248 (mm) cc_final: 0.5399 (mm) REVERT: 1 173 TYR cc_start: 0.6166 (t80) cc_final: 0.5417 (t80) REVERT: 1 193 GLU cc_start: 0.6370 (tm-30) cc_final: 0.6092 (tm-30) REVERT: 2 45 ILE cc_start: 0.7202 (tt) cc_final: 0.6720 (tt) REVERT: 2 48 ILE cc_start: 0.8531 (mm) cc_final: 0.8152 (mm) REVERT: 2 52 MET cc_start: 0.5779 (ttm) cc_final: 0.5426 (ttt) REVERT: 2 55 THR cc_start: 0.7523 (p) cc_final: 0.7307 (p) REVERT: 2 86 THR cc_start: 0.8594 (t) cc_final: 0.7991 (t) REVERT: 2 116 ASP cc_start: 0.6356 (p0) cc_final: 0.5688 (p0) REVERT: 2 190 LYS cc_start: 0.8000 (tptp) cc_final: 0.7770 (tptt) REVERT: 3 46 TYR cc_start: 0.7593 (m-80) cc_final: 0.6973 (m-80) REVERT: 3 90 ILE cc_start: 0.8863 (tt) cc_final: 0.8584 (tt) REVERT: 4 48 ILE cc_start: 0.9204 (mm) cc_final: 0.8886 (mm) REVERT: 4 68 ARG cc_start: 0.8602 (tpp80) cc_final: 0.8263 (tpp80) REVERT: 4 123 TYR cc_start: 0.8818 (m-80) cc_final: 0.8047 (m-80) REVERT: 4 137 ILE cc_start: 0.8203 (mm) cc_final: 0.7597 (tt) REVERT: 4 191 ILE cc_start: 0.7836 (tp) cc_final: 0.7613 (tp) REVERT: 5 46 TYR cc_start: 0.7740 (m-80) cc_final: 0.7394 (m-10) REVERT: 5 120 LYS cc_start: 0.7250 (mtmm) cc_final: 0.7032 (mttp) REVERT: 5 191 ILE cc_start: 0.7253 (mt) cc_final: 0.6981 (mt) REVERT: 5 192 THR cc_start: 0.6741 (t) cc_final: 0.6462 (t) REVERT: 6 81 ARG cc_start: 0.7574 (ttm110) cc_final: 0.7308 (mmt90) REVERT: 6 90 ILE cc_start: 0.8990 (mm) cc_final: 0.8670 (mm) REVERT: 7 116 ASP cc_start: 0.7240 (p0) cc_final: 0.6910 (p0) outliers start: 1 outliers final: 0 residues processed: 1228 average time/residue: 0.3526 time to fit residues: 671.7851 Evaluate side-chains 1130 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1129 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 0.9990 chunk 284 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 chunk 276 optimal weight: 0.0980 chunk 166 optimal weight: 0.3980 chunk 120 optimal weight: 0.9990 chunk 217 optimal weight: 0.0980 chunk 84 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 275 optimal weight: 0.6980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 5 GLN ** 1 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 198 GLN 3 99 ASN 7 198 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.7739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24968 Z= 0.240 Angle : 0.714 13.599 33660 Z= 0.380 Chirality : 0.049 0.293 3881 Planarity : 0.004 0.052 4329 Dihedral : 5.539 40.158 3498 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.94 % Favored : 95.87 % Rotamer: Outliers : 0.08 % Allowed : 0.73 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: -0.63 (0.15), residues: 3122 helix: 0.31 (0.15), residues: 1231 sheet: -0.04 (0.19), residues: 609 loop : -1.25 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS G 73 PHE 0.028 0.002 PHE 5 196 TYR 0.035 0.002 TYR 5 123 ARG 0.012 0.001 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1213 time to evaluate : 2.908 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: A 36 THR cc_start: 0.9470 (m) cc_final: 0.9242 (m) REVERT: A 117 CYS cc_start: 0.8722 (m) cc_final: 0.8503 (m) REVERT: A 121 GLN cc_start: 0.7781 (tp40) cc_final: 0.7391 (tp40) REVERT: A 186 ASP cc_start: 0.6320 (p0) cc_final: 0.5782 (p0) REVERT: A 208 ASN cc_start: 0.7609 (p0) cc_final: 0.7139 (p0) REVERT: A 211 VAL cc_start: 0.8466 (t) cc_final: 0.7639 (p) REVERT: B 6 MET cc_start: 0.6727 (pmm) cc_final: 0.5394 (ptp) REVERT: B 8 TYR cc_start: 0.7619 (m-80) cc_final: 0.7370 (m-80) REVERT: B 36 THR cc_start: 0.8295 (m) cc_final: 0.8093 (m) REVERT: B 58 LEU cc_start: 0.7949 (mt) cc_final: 0.7739 (mt) REVERT: B 98 ILE cc_start: 0.8335 (mm) cc_final: 0.8125 (mm) REVERT: B 181 ASP cc_start: 0.7158 (m-30) cc_final: 0.6910 (m-30) REVERT: B 201 GLU cc_start: 0.5679 (tm-30) cc_final: 0.5422 (tm-30) REVERT: C 9 ASP cc_start: 0.6900 (p0) cc_final: 0.6689 (p0) REVERT: C 52 LYS cc_start: 0.7429 (tttt) cc_final: 0.7107 (tttt) REVERT: C 114 LYS cc_start: 0.7626 (mtpp) cc_final: 0.7368 (mtpp) REVERT: C 175 PHE cc_start: 0.7759 (m-80) cc_final: 0.7458 (m-80) REVERT: C 182 ASP cc_start: 0.6252 (p0) cc_final: 0.5624 (p0) REVERT: C 184 SER cc_start: 0.5630 (p) cc_final: 0.4978 (m) REVERT: C 196 MET cc_start: 0.6325 (mtt) cc_final: 0.5920 (mtt) REVERT: C 202 SER cc_start: 0.7785 (p) cc_final: 0.7477 (p) REVERT: C 214 VAL cc_start: 0.8522 (t) cc_final: 0.8310 (t) REVERT: C 217 ASP cc_start: 0.7504 (p0) cc_final: 0.7192 (p0) REVERT: D 57 LYS cc_start: 0.7748 (pttm) cc_final: 0.7277 (mppt) REVERT: D 91 ARG cc_start: 0.8441 (tpt90) cc_final: 0.7943 (tpt170) REVERT: D 240 ILE cc_start: 0.7563 (pt) cc_final: 0.7167 (pt) REVERT: E 6 MET cc_start: 0.7345 (ttt) cc_final: 0.7144 (ttm) REVERT: E 8 TYR cc_start: 0.7432 (m-10) cc_final: 0.6578 (m-80) REVERT: E 25 GLU cc_start: 0.6474 (tp30) cc_final: 0.5936 (tp30) REVERT: E 28 ARG cc_start: 0.8099 (mmm160) cc_final: 0.7438 (mmm160) REVERT: E 74 ILE cc_start: 0.8440 (mp) cc_final: 0.8226 (mp) REVERT: E 186 ASP cc_start: 0.6150 (m-30) cc_final: 0.5434 (m-30) REVERT: E 200 ILE cc_start: 0.8502 (pt) cc_final: 0.8011 (pt) REVERT: E 218 ASP cc_start: 0.8510 (p0) cc_final: 0.7851 (p0) REVERT: F 9 ASP cc_start: 0.8317 (p0) cc_final: 0.7525 (p0) REVERT: G 5 GLN cc_start: 0.6249 (OUTLIER) cc_final: 0.4888 (pt0) REVERT: G 21 LEU cc_start: 0.8209 (pp) cc_final: 0.7996 (pp) REVERT: G 73 HIS cc_start: 0.7043 (p-80) cc_final: 0.6561 (p90) REVERT: G 151 ASP cc_start: 0.8774 (t0) cc_final: 0.8570 (t0) REVERT: G 174 PHE cc_start: 0.7482 (t80) cc_final: 0.7108 (t80) REVERT: G 191 LEU cc_start: 0.7521 (tp) cc_final: 0.7091 (tp) REVERT: G 196 MET cc_start: 0.6847 (tpp) cc_final: 0.6497 (tpp) REVERT: G 211 VAL cc_start: 0.9095 (t) cc_final: 0.8798 (p) REVERT: G 234 GLU cc_start: 0.6137 (pp20) cc_final: 0.5713 (pp20) REVERT: 1 43 LYS cc_start: 0.6914 (ttmm) cc_final: 0.6674 (tttm) REVERT: 1 68 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.8147 (ttm-80) REVERT: 1 122 ILE cc_start: 0.7575 (mm) cc_final: 0.7314 (mm) REVERT: 1 172 ILE cc_start: 0.6087 (mm) cc_final: 0.5348 (mm) REVERT: 1 173 TYR cc_start: 0.6171 (t80) cc_final: 0.5420 (t80) REVERT: 1 193 GLU cc_start: 0.6436 (tm-30) cc_final: 0.5967 (tm-30) REVERT: 2 45 ILE cc_start: 0.7572 (tt) cc_final: 0.7059 (tt) REVERT: 2 48 ILE cc_start: 0.8444 (mm) cc_final: 0.8072 (mm) REVERT: 2 52 MET cc_start: 0.5715 (ttm) cc_final: 0.5161 (ttt) REVERT: 2 86 THR cc_start: 0.8626 (t) cc_final: 0.8090 (t) REVERT: 2 116 ASP cc_start: 0.6419 (p0) cc_final: 0.5791 (p0) REVERT: 2 190 LYS cc_start: 0.7931 (tptp) cc_final: 0.7615 (tptp) REVERT: 3 44 LYS cc_start: 0.7327 (tptt) cc_final: 0.7117 (mptt) REVERT: 3 46 TYR cc_start: 0.7370 (m-80) cc_final: 0.6725 (m-80) REVERT: 3 87 VAL cc_start: 0.8408 (t) cc_final: 0.8049 (t) REVERT: 3 88 ARG cc_start: 0.6086 (mtp85) cc_final: 0.5585 (mtp85) REVERT: 3 123 TYR cc_start: 0.8208 (m-10) cc_final: 0.7717 (m-80) REVERT: 4 48 ILE cc_start: 0.9191 (mm) cc_final: 0.8789 (mm) REVERT: 4 123 TYR cc_start: 0.8788 (m-80) cc_final: 0.8051 (m-80) REVERT: 4 203 GLU cc_start: 0.2070 (mm-30) cc_final: 0.1856 (mm-30) REVERT: 4 206 GLN cc_start: 0.5035 (mt0) cc_final: 0.4775 (mm-40) REVERT: 5 46 TYR cc_start: 0.7600 (m-80) cc_final: 0.7383 (m-10) REVERT: 6 79 ILE cc_start: 0.8867 (mt) cc_final: 0.8498 (mt) REVERT: 6 81 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7263 (mmt90) REVERT: 6 90 ILE cc_start: 0.9002 (mm) cc_final: 0.8673 (mm) REVERT: 6 116 ASP cc_start: 0.8282 (p0) cc_final: 0.8018 (p0) REVERT: 6 120 LYS cc_start: 0.6069 (mttt) cc_final: 0.5519 (mttm) REVERT: 6 207 ILE cc_start: 0.5775 (pt) cc_final: 0.5478 (pt) REVERT: 7 116 ASP cc_start: 0.7251 (p0) cc_final: 0.7040 (p0) outliers start: 2 outliers final: 0 residues processed: 1215 average time/residue: 0.3520 time to fit residues: 661.0677 Evaluate side-chains 1111 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1110 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.7980 chunk 292 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 138 optimal weight: 0.0170 chunk 203 optimal weight: 0.6980 chunk 306 optimal weight: 0.6980 chunk 282 optimal weight: 0.0980 chunk 244 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 188 optimal weight: 0.9980 chunk 149 optimal weight: 0.0770 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 5 GLN 1 198 GLN 2 198 GLN 3 75 ASN 4 75 ASN ** 4 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 198 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.7849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24968 Z= 0.227 Angle : 0.726 13.349 33660 Z= 0.386 Chirality : 0.049 0.331 3881 Planarity : 0.004 0.071 4329 Dihedral : 5.481 38.763 3498 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.84 % Favored : 95.96 % Rotamer: Outliers : 0.08 % Allowed : 0.31 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3122 helix: 0.30 (0.15), residues: 1245 sheet: -0.02 (0.19), residues: 610 loop : -1.20 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 73 PHE 0.029 0.002 PHE A 221 TYR 0.035 0.002 TYR E 232 ARG 0.015 0.001 ARG E 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1188 time to evaluate : 2.566 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: A 98 ILE cc_start: 0.8403 (mt) cc_final: 0.8139 (mt) REVERT: A 121 GLN cc_start: 0.7792 (tp40) cc_final: 0.7511 (tp40) REVERT: A 208 ASN cc_start: 0.7460 (p0) cc_final: 0.6884 (p0) REVERT: A 211 VAL cc_start: 0.8459 (t) cc_final: 0.7552 (p) REVERT: B 6 MET cc_start: 0.6770 (pmm) cc_final: 0.5425 (ptp) REVERT: B 58 LEU cc_start: 0.7932 (mt) cc_final: 0.7728 (mt) REVERT: B 93 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.7680 (mtt-85) REVERT: C 52 LYS cc_start: 0.7385 (tttt) cc_final: 0.6998 (tttt) REVERT: C 182 ASP cc_start: 0.6137 (p0) cc_final: 0.5312 (p0) REVERT: C 184 SER cc_start: 0.5779 (p) cc_final: 0.5196 (m) REVERT: C 196 MET cc_start: 0.5948 (mtt) cc_final: 0.5747 (mtt) REVERT: C 214 VAL cc_start: 0.8452 (t) cc_final: 0.8179 (t) REVERT: C 217 ASP cc_start: 0.7511 (p0) cc_final: 0.7212 (p0) REVERT: D 57 LYS cc_start: 0.8040 (pttm) cc_final: 0.7420 (mppt) REVERT: D 91 ARG cc_start: 0.8423 (tpt90) cc_final: 0.8116 (tpt170) REVERT: E 6 MET cc_start: 0.7329 (ttt) cc_final: 0.7129 (ttm) REVERT: E 8 TYR cc_start: 0.7375 (m-10) cc_final: 0.6537 (m-80) REVERT: E 25 GLU cc_start: 0.6424 (tp30) cc_final: 0.5859 (tp30) REVERT: E 52 LYS cc_start: 0.7131 (pttm) cc_final: 0.6554 (pttp) REVERT: E 186 ASP cc_start: 0.5940 (m-30) cc_final: 0.5405 (m-30) REVERT: E 200 ILE cc_start: 0.8378 (pt) cc_final: 0.7919 (pt) REVERT: E 218 ASP cc_start: 0.8534 (p0) cc_final: 0.7993 (p0) REVERT: F 9 ASP cc_start: 0.8222 (p0) cc_final: 0.7605 (p0) REVERT: F 107 ILE cc_start: 0.8997 (tt) cc_final: 0.8649 (tt) REVERT: F 112 LEU cc_start: 0.9137 (tp) cc_final: 0.8881 (tp) REVERT: G 73 HIS cc_start: 0.7030 (p-80) cc_final: 0.6718 (p90) REVERT: G 151 ASP cc_start: 0.8798 (t0) cc_final: 0.8473 (t0) REVERT: G 176 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6447 (mm-30) REVERT: G 191 LEU cc_start: 0.7600 (tp) cc_final: 0.7395 (tp) REVERT: G 196 MET cc_start: 0.6948 (tpp) cc_final: 0.6500 (tpp) REVERT: G 234 GLU cc_start: 0.6244 (pp20) cc_final: 0.5817 (pp20) REVERT: 1 68 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.8149 (ttm-80) REVERT: 1 172 ILE cc_start: 0.5889 (mm) cc_final: 0.5247 (mm) REVERT: 1 173 TYR cc_start: 0.6266 (t80) cc_final: 0.5490 (t80) REVERT: 1 193 GLU cc_start: 0.6239 (tm-30) cc_final: 0.5938 (tm-30) REVERT: 2 45 ILE cc_start: 0.7589 (tt) cc_final: 0.7020 (tt) REVERT: 2 48 ILE cc_start: 0.8538 (mm) cc_final: 0.8165 (mm) REVERT: 2 52 MET cc_start: 0.5649 (ttm) cc_final: 0.5260 (ttm) REVERT: 2 86 THR cc_start: 0.8662 (t) cc_final: 0.8187 (t) REVERT: 2 116 ASP cc_start: 0.6406 (p0) cc_final: 0.5824 (p0) REVERT: 2 190 LYS cc_start: 0.7970 (tptp) cc_final: 0.7630 (tptp) REVERT: 3 44 LYS cc_start: 0.7211 (tptt) cc_final: 0.6981 (mptt) REVERT: 3 46 TYR cc_start: 0.7258 (m-80) cc_final: 0.6755 (m-80) REVERT: 3 87 VAL cc_start: 0.8459 (t) cc_final: 0.7995 (t) REVERT: 3 88 ARG cc_start: 0.6339 (mtp85) cc_final: 0.5503 (mtp85) REVERT: 3 123 TYR cc_start: 0.8123 (m-10) cc_final: 0.7911 (m-80) REVERT: 4 48 ILE cc_start: 0.9130 (mm) cc_final: 0.8801 (mm) REVERT: 4 68 ARG cc_start: 0.8592 (tpp80) cc_final: 0.8291 (tpp80) REVERT: 4 123 TYR cc_start: 0.8761 (m-80) cc_final: 0.8066 (m-80) REVERT: 5 142 SER cc_start: 0.6811 (t) cc_final: 0.6512 (t) REVERT: 5 189 VAL cc_start: 0.7257 (m) cc_final: 0.7012 (m) REVERT: 6 81 ARG cc_start: 0.7501 (ttm110) cc_final: 0.7281 (mmt90) REVERT: 6 90 ILE cc_start: 0.8990 (mm) cc_final: 0.8643 (mm) REVERT: 6 116 ASP cc_start: 0.8202 (p0) cc_final: 0.7909 (p0) REVERT: 6 120 LYS cc_start: 0.5927 (mttt) cc_final: 0.5403 (mttm) REVERT: 7 33 MET cc_start: 0.2396 (mmt) cc_final: 0.0869 (mtt) REVERT: 7 116 ASP cc_start: 0.7160 (p0) cc_final: 0.6876 (p0) REVERT: 7 190 LYS cc_start: 0.7315 (pttp) cc_final: 0.7109 (pttp) outliers start: 2 outliers final: 1 residues processed: 1189 average time/residue: 0.3412 time to fit residues: 632.5844 Evaluate side-chains 1092 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1091 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 0.7980 chunk 260 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 225 optimal weight: 5.9990 chunk 36 optimal weight: 0.0010 chunk 67 optimal weight: 1.9990 chunk 244 optimal weight: 0.0770 chunk 102 optimal weight: 0.9980 chunk 251 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 overall best weight: 0.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 5 GLN ** 1 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 198 GLN 3 75 ASN 4 75 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.176770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.144781 restraints weight = 36566.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.149139 restraints weight = 21007.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.152036 restraints weight = 14103.326| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.7992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24968 Z= 0.245 Angle : 0.727 13.115 33660 Z= 0.386 Chirality : 0.049 0.307 3881 Planarity : 0.004 0.062 4329 Dihedral : 5.513 38.909 3498 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.97 % Favored : 95.87 % Rotamer: Outliers : 0.04 % Allowed : 0.42 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3122 helix: 0.35 (0.15), residues: 1228 sheet: -0.14 (0.19), residues: 611 loop : -1.17 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 73 PHE 0.030 0.002 PHE A 221 TYR 0.034 0.002 TYR 7 148 ARG 0.015 0.001 ARG A 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9708.31 seconds wall clock time: 171 minutes 48.87 seconds (10308.87 seconds total)