Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 05:49:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/04_2023/6he5_0210.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/04_2023/6he5_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_0210/04_2023/6he5_0210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/04_2023/6he5_0210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/04_2023/6he5_0210.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/04_2023/6he5_0210.pdb" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 12.77, per 1000 atoms: 0.52 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: 9.72 Conformation dependent library (CDL) restraints added in 3.7 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: 1.39 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: 8.26 Time building geometry restraints manager: 10.53 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: 2.360 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: 0.030 Extract box with map and model: 13.430 Check model and map are aligned: 0.390 Set scattering table: 0.210 Process input model: 61.690 Find NCS groups from input model: 1.600 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.880 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 3.015 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 outliers start: 118 outliers final: 19 residues processed: 1361 average time/residue: 0.4202 time to fit residues: 840.1464 Evaluate side-chains 1100 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1081 time to evaluate : 2.617 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.2161 time to fit residues: 11.4134 ------------------------------------------------------------------------------- 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: 2.9990 chunk 129 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 157 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 241 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 279 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** D 169 ASN F 99 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 Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.113 24968 Z= 0.323 Angle : 0.859 14.263 33660 Z= 0.471 Chirality : 0.051 0.218 3881 Planarity : 0.006 0.076 4329 Dihedral : 6.552 57.097 3498 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.59 % Favored : 96.09 % Rotamer Outliers : 0.34 % 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: -1.22 (0.14), residues: 3122 helix: 0.00 (0.14), residues: 1236 sheet: 0.15 (0.19), residues: 592 loop : -2.08 (0.15), residues: 1294 *********************** 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 1293 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1284 time to evaluate : 3.008 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 outliers start: 9 outliers final: 0 residues processed: 1289 average time/residue: 0.4045 time to fit residues: 784.0627 Evaluate side-chains 1085 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1085 time to evaluate : 2.862 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0827 ------------------------------------------------------------------------------- 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: 0.2980 chunk 86 optimal weight: 0.9980 chunk 232 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 280 optimal weight: 4.9990 chunk 302 optimal weight: 0.0170 chunk 249 optimal weight: 0.8980 chunk 277 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN D 237 ASN F 99 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 75 ASN 5 109 GLN 5 198 GLN 6 96 ASN 6 198 GLN 7 96 ASN 7 198 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 24968 Z= 0.278 Angle : 0.749 14.269 33660 Z= 0.408 Chirality : 0.049 0.214 3881 Planarity : 0.005 0.054 4329 Dihedral : 5.924 51.381 3498 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.20 % Favored : 95.48 % Rotamer Outliers : 0.31 % 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: -0.89 (0.14), residues: 3122 helix: 0.14 (0.14), residues: 1225 sheet: 0.28 (0.19), residues: 596 loop : -1.71 (0.15), residues: 1301 *********************** 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 1256 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1248 time to evaluate : 2.924 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 outliers start: 8 outliers final: 1 residues processed: 1251 average time/residue: 0.3963 time to fit residues: 753.3278 Evaluate side-chains 1110 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1109 time to evaluate : 2.629 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3535 time to fit residues: 4.7304 ------------------------------------------------------------------------------- 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: 4.9990 chunk 145 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 188 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 297 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 chunk 266 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN D 237 ASN F 99 ASN F 237 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN 3 64 GLN 3 75 ASN 4 75 ASN 6 75 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.6374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 24968 Z= 0.289 Angle : 0.728 14.381 33660 Z= 0.393 Chirality : 0.048 0.210 3881 Planarity : 0.005 0.053 4329 Dihedral : 5.767 49.645 3498 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.13 % Favored : 95.55 % Rotamer Outliers : 0.19 % 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: -0.77 (0.14), residues: 3122 helix: 0.23 (0.14), residues: 1215 sheet: 0.16 (0.19), residues: 614 loop : -1.53 (0.16), residues: 1293 *********************** 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 1228 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1223 time to evaluate : 2.777 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 outliers start: 5 outliers final: 0 residues processed: 1225 average time/residue: 0.3751 time to fit residues: 702.1052 Evaluate side-chains 1099 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1099 time to evaluate : 2.620 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7361 ------------------------------------------------------------------------------- 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: 0.8980 chunk 168 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 254 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 267 optimal weight: 0.8980 chunk 75 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN F 5 GLN F 99 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN 2 198 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.6924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 24968 Z= 0.289 Angle : 0.729 14.483 33660 Z= 0.391 Chirality : 0.048 0.235 3881 Planarity : 0.004 0.048 4329 Dihedral : 5.701 49.403 3498 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.10 % Favored : 95.64 % Rotamer Outliers : 0.15 % 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: -0.72 (0.14), residues: 3122 helix: 0.25 (0.14), residues: 1241 sheet: 0.14 (0.19), residues: 625 loop : -1.49 (0.16), residues: 1256 *********************** 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 1241 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1237 time to evaluate : 2.710 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 outliers start: 4 outliers final: 0 residues processed: 1239 average time/residue: 0.3706 time to fit residues: 706.0903 Evaluate side-chains 1105 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1105 time to evaluate : 3.022 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2701 ------------------------------------------------------------------------------- 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: 0.7980 chunk 268 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 169 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN F 99 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 198 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 99 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.7352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 24968 Z= 0.311 Angle : 0.738 14.301 33660 Z= 0.395 Chirality : 0.048 0.272 3881 Planarity : 0.004 0.041 4329 Dihedral : 5.752 50.974 3498 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.20 % Favored : 95.61 % Rotamer Outliers : 0.00 % 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: -0.69 (0.14), residues: 3122 helix: 0.27 (0.14), residues: 1232 sheet: 0.15 (0.19), residues: 615 loop : -1.44 (0.16), residues: 1275 *********************** 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 1244 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1244 time to evaluate : 3.174 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 outliers start: 0 outliers final: 0 residues processed: 1244 average time/residue: 0.3878 time to fit residues: 746.3196 Evaluate side-chains 1103 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1103 time to evaluate : 3.109 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3409 ------------------------------------------------------------------------------- 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: 0.2980 chunk 33 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 166 optimal weight: 0.0670 chunk 296 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 169 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN D 237 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 198 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 75 ASN ** 7 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.7581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 24968 Z= 0.276 Angle : 0.730 13.950 33660 Z= 0.388 Chirality : 0.049 0.233 3881 Planarity : 0.004 0.063 4329 Dihedral : 5.654 45.404 3498 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.16 % Favored : 95.64 % Rotamer Outliers : 0.00 % 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: -0.76 (0.14), residues: 3122 helix: 0.28 (0.15), residues: 1209 sheet: 0.04 (0.19), residues: 618 loop : -1.48 (0.16), residues: 1295 *********************** 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 1221 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1221 time to evaluate : 2.998 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 outliers start: 0 outliers final: 0 residues processed: 1221 average time/residue: 0.3784 time to fit residues: 719.5963 Evaluate side-chains 1100 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1100 time to evaluate : 2.809 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9585 ------------------------------------------------------------------------------- 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: 0.6980 chunk 118 optimal weight: 0.3980 chunk 177 optimal weight: 0.9980 chunk 89 optimal weight: 0.0980 chunk 58 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 202 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 233 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 64 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 75 ASN ** 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: 0.6877 moved from start: 0.7738 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= 0.259 Angle : 0.730 13.689 33660 Z= 0.388 Chirality : 0.049 0.302 3881 Planarity : 0.004 0.056 4329 Dihedral : 5.646 45.687 3498 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.13 % Favored : 95.68 % Rotamer Outliers : 0.00 % 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: -0.77 (0.14), residues: 3122 helix: 0.25 (0.14), residues: 1242 sheet: -0.06 (0.19), residues: 618 loop : -1.45 (0.16), residues: 1262 *********************** 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 1199 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1199 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1199 average time/residue: 0.3581 time to fit residues: 674.0910 Evaluate side-chains 1099 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1099 time to evaluate : 2.873 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0910 ------------------------------------------------------------------------------- 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: 0.9980 chunk 284 optimal weight: 0.9980 chunk 259 optimal weight: 0.7980 chunk 276 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 217 optimal weight: 0.7980 chunk 84 optimal weight: 0.0770 chunk 249 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 275 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.7934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 24968 Z= 0.291 Angle : 0.760 13.650 33660 Z= 0.404 Chirality : 0.050 0.368 3881 Planarity : 0.004 0.043 4329 Dihedral : 5.670 45.949 3498 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.23 % Favored : 95.55 % Rotamer Outliers : 0.00 % 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: -0.86 (0.14), residues: 3122 helix: 0.17 (0.14), residues: 1241 sheet: -0.15 (0.19), residues: 620 loop : -1.48 (0.16), residues: 1261 *********************** 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 1209 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1209 time to evaluate : 2.817 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 outliers start: 0 outliers final: 0 residues processed: 1209 average time/residue: 0.3610 time to fit residues: 679.3928 Evaluate side-chains 1092 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1092 time to evaluate : 2.605 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6993 ------------------------------------------------------------------------------- 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: 0.6980 chunk 292 optimal weight: 0.4980 chunk 178 optimal weight: 0.1980 chunk 138 optimal weight: 0.5980 chunk 203 optimal weight: 0.5980 chunk 306 optimal weight: 0.4980 chunk 282 optimal weight: 0.1980 chunk 244 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 chunk 149 optimal weight: 0.0770 overall best weight: 0.2938 ------------------------------------------------------------------------------- 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 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN ** 1 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 198 GLN 3 75 ASN 5 64 GLN 5 198 GLN ** 7 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.8043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 24968 Z= 0.241 Angle : 0.751 13.155 33660 Z= 0.398 Chirality : 0.050 0.324 3881 Planarity : 0.004 0.070 4329 Dihedral : 5.611 46.346 3498 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.16 % Favored : 95.64 % Rotamer Outliers : 0.00 % 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: -0.78 (0.14), residues: 3122 helix: 0.18 (0.14), residues: 1244 sheet: -0.02 (0.19), residues: 600 loop : -1.39 (0.16), residues: 1278 ********************** 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 1184 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1184 time to evaluate : 3.148 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 outliers start: 0 outliers final: 0 residues processed: 1184 average time/residue: 0.3553 time to fit residues: 660.5825 Evaluate side-chains 1095 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1095 time to evaluate : 2.738 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9245 ------------------------------------------------------------------------------- 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: 0.5980 chunk 260 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 225 optimal weight: 0.6980 chunk 36 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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** ** A 208 ASN ** 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 ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN 3 75 ASN 5 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.174891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.141886 restraints weight = 36641.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.146110 restraints weight = 21305.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.148956 restraints weight = 14510.119| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.8230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 24968 Z= 0.291 Angle : 0.768 13.288 33660 Z= 0.406 Chirality : 0.050 0.320 3881 Planarity : 0.005 0.089 4329 Dihedral : 5.701 44.334 3498 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.39 % Favored : 95.42 % Rotamer Outliers : 0.00 % 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: -0.85 (0.14), residues: 3122 helix: 0.10 (0.14), residues: 1241 sheet: -0.11 (0.19), residues: 606 loop : -1.38 (0.16), residues: 1275 =============================================================================== Job complete usr+sys time: 9733.73 seconds wall clock time: 173 minutes 41.52 seconds (10421.52 seconds total)