Starting phenix.real_space_refine on Tue Mar 19 09:45:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he7_0211/03_2024/6he7_0211.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he7_0211/03_2024/6he7_0211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he7_0211/03_2024/6he7_0211.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he7_0211/03_2024/6he7_0211.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he7_0211/03_2024/6he7_0211.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he7_0211/03_2024/6he7_0211.pdb" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 15113 2.51 5 N 3990 2.21 5 O 4634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 186": "OD1" <-> "OD2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 104": "OD1" <-> "OD2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 104": "OD1" <-> "OD2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 142": "OD1" <-> "OD2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "C PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ASP 182": "OD1" <-> "OD2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 235": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 241": "NH1" <-> "NH2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D ASP 84": "OD1" <-> "OD2" Residue "D ASP 90": "OD1" <-> "OD2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "D TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 142": "OD1" <-> "OD2" Residue "D TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 151": "OD1" <-> "OD2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ASP 186": "OD1" <-> "OD2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D ASP 218": "OD1" <-> "OD2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 241": "NH1" <-> "NH2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 18": "OD1" <-> "OD2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E ASP 51": "OD1" <-> "OD2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 149": "OE1" <-> "OE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 180": "NH1" <-> "NH2" Residue "E ASP 181": "OD1" <-> "OD2" Residue "E ASP 186": "OD1" <-> "OD2" Residue "E TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 218": "OD1" <-> "OD2" Residue "E TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E ARG 241": "NH1" <-> "NH2" Residue "E GLU 242": "OE1" <-> "OE2" Residue "F PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 18": "OD1" <-> "OD2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F ASP 71": "OD1" <-> "OD2" Residue "F ASP 90": "OD1" <-> "OD2" Residue "F TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "F TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F GLU 149": "OE1" <-> "OE2" Residue "F TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "F PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 180": "NH1" <-> "NH2" Residue "F ASP 181": "OD1" <-> "OD2" Residue "F ASP 182": "OD1" <-> "OD2" Residue "F ASP 187": "OD1" <-> "OD2" Residue "F ASP 218": "OD1" <-> "OD2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "F TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 234": "OE1" <-> "OE2" Residue "F ARG 235": "NH1" <-> "NH2" Residue "F GLU 238": "OE1" <-> "OE2" Residue "F ARG 239": "NH1" <-> "NH2" Residue "F ARG 241": "NH1" <-> "NH2" Residue "G GLU 25": "OE1" <-> "OE2" Residue "G ASP 51": "OD1" <-> "OD2" Residue "G ASP 62": "OD1" <-> "OD2" Residue "G GLU 65": "OE1" <-> "OE2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "G TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 142": "OD1" <-> "OD2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "G PHE 174": "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 187": "OD1" <-> "OD2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 218": "OD1" <-> "OD2" Residue "G GLU 227": "OE1" <-> "OE2" Residue "G TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 235": "NH1" <-> "NH2" Residue "G ARG 239": "NH1" <-> "NH2" Residue "G ARG 241": "NH1" <-> "NH2" 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 GLU 82": "OE1" <-> "OE2" Residue "1 ARG 88": "NH1" <-> "NH2" Residue "1 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 102": "NH1" <-> "NH2" Residue "1 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 154": "NH1" <-> "NH2" Residue "1 PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 162": "OD1" <-> "OD2" Residue "1 GLU 163": "OE1" <-> "OE2" Residue "1 ARG 170": "NH1" <-> "NH2" Residue "1 ASP 179": "OD1" <-> "OD2" Residue "1 GLU 195": "OE1" <-> "OE2" Residue "1 PHE 196": "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 ASP 50": "OD1" <-> "OD2" Residue "2 ARG 51": "NH1" <-> "NH2" Residue "2 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 102": "NH1" <-> "NH2" Residue "2 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 134": "OE1" <-> "OE2" Residue "2 GLU 152": "OE1" <-> "OE2" Residue "2 ARG 154": "NH1" <-> "NH2" Residue "2 PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 162": "OD1" <-> "OD2" Residue "2 ARG 170": "NH1" <-> "NH2" Residue "2 ASP 179": "OD1" <-> "OD2" Residue "2 ASP 184": "OD1" <-> "OD2" Residue "2 ASP 187": "OD1" <-> "OD2" Residue "2 GLU 195": "OE1" <-> "OE2" Residue "2 PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 21": "OD1" <-> "OD2" Residue "3 ARG 30": "NH1" <-> "NH2" Residue "3 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 50": "OD1" <-> "OD2" Residue "3 ARG 51": "NH1" <-> "NH2" Residue "3 ASP 62": "OD1" <-> "OD2" Residue "3 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 80": "NH1" <-> "NH2" Residue "3 GLU 82": "OE1" <-> "OE2" Residue "3 ARG 83": "NH1" <-> "NH2" Residue "3 ARG 102": "NH1" <-> "NH2" Residue "3 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 118": "OE1" <-> "OE2" Residue "3 ASP 126": "OD1" <-> "OD2" Residue "3 ASP 136": "OD1" <-> "OD2" Residue "3 GLU 152": "OE1" <-> "OE2" Residue "3 ASP 162": "OD1" <-> "OD2" Residue "3 GLU 166": "OE1" <-> "OE2" Residue "3 ASP 179": "OD1" <-> "OD2" Residue "3 GLU 193": "OE1" <-> "OE2" Residue "3 ASP 194": "OD1" <-> "OD2" Residue "3 GLU 195": "OE1" <-> "OE2" Residue "3 PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 202": "OE1" <-> "OE2" Residue "3 GLU 203": "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 ARG 51": "NH1" <-> "NH2" Residue "4 GLU 73": "OE1" <-> "OE2" Residue "4 TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 78": "OE1" <-> "OE2" Residue "4 GLU 82": "OE1" <-> "OE2" Residue "4 ARG 83": "NH1" <-> "NH2" Residue "4 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 102": "NH1" <-> "NH2" Residue "4 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 116": "OD1" <-> "OD2" Residue "4 TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 152": "OE1" <-> "OE2" Residue "4 ASP 153": "OD1" <-> "OD2" Residue "4 ARG 154": "NH1" <-> "NH2" Residue "4 ASP 162": "OD1" <-> "OD2" Residue "4 GLU 166": "OE1" <-> "OE2" Residue "4 GLU 193": "OE1" <-> "OE2" Residue "4 PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 202": "OE1" <-> "OE2" Residue "4 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 21": "OD1" <-> "OD2" Residue "5 GLU 28": "OE1" <-> "OE2" Residue "5 ARG 30": "NH1" <-> "NH2" Residue "5 ARG 51": "NH1" <-> "NH2" Residue "5 TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 88": "NH1" <-> "NH2" Residue "5 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 102": "NH1" <-> "NH2" Residue "5 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 152": "OE1" <-> "OE2" Residue "5 ARG 154": "NH1" <-> "NH2" Residue "5 ASP 179": "OD1" <-> "OD2" Residue "5 ASP 187": "OD1" <-> "OD2" Residue "5 TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 202": "OE1" <-> "OE2" Residue "5 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 28": "OE1" <-> "OE2" Residue "6 ARG 30": "NH1" <-> "NH2" Residue "6 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 50": "OD1" <-> "OD2" Residue "6 ARG 51": "NH1" <-> "NH2" Residue "6 TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 78": "OE1" <-> "OE2" Residue "6 ARG 80": "NH1" <-> "NH2" Residue "6 GLU 82": "OE1" <-> "OE2" Residue "6 ARG 83": "NH1" <-> "NH2" Residue "6 ARG 88": "NH1" <-> "NH2" Residue "6 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 154": "NH1" <-> "NH2" Residue "6 GLU 158": "OE1" <-> "OE2" Residue "6 GLU 163": "OE1" <-> "OE2" Residue "6 ASP 184": "OD1" <-> "OD2" Residue "6 GLU 195": "OE1" <-> "OE2" Residue "6 TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 203": "OE1" <-> "OE2" Residue "6 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 21": "OD1" <-> "OD2" Residue "7 GLU 28": "OE1" <-> "OE2" Residue "7 ARG 30": "NH1" <-> "NH2" Residue "7 ASP 50": "OD1" <-> "OD2" Residue "7 ARG 51": "NH1" <-> "NH2" Residue "7 GLU 73": "OE1" <-> "OE2" 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 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 116": "OD1" <-> "OD2" Residue "7 TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 133": "OE1" <-> "OE2" Residue "7 ASP 153": "OD1" <-> "OD2" Residue "7 ARG 154": "NH1" <-> "NH2" Residue "7 PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 158": "OE1" <-> "OE2" Residue "7 GLU 163": "OE1" <-> "OE2" 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 GLU 203": "OE1" <-> "OE2" Residue "7 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23821 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "B" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "C" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "D" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "E" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "F" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "G" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "1" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "2" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "3" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain: "4" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "5" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "6" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain: "7" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Time building chain proxies: 11.60, per 1000 atoms: 0.49 Number of scatterers: 23821 At special positions: 0 Unit cell: (134, 134, 104.52, 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 84 16.00 O 4634 8.00 N 3990 7.00 C 15113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.17 Conformation dependent library (CDL) restraints added in 4.3 seconds 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5670 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 30 sheets defined 43.1% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 Processing helix chain 'A' and resid 81 through 104 Processing helix chain 'A' and resid 108 through 126 removed outlier: 3.745A pdb=" N PHE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 179 removed outlier: 4.041A pdb=" N LYS A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 201 Processing helix chain 'A' and resid 225 through 244 Proline residue: A 231 - end of helix removed outlier: 3.775A pdb=" N GLU A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 81 through 104 Processing helix chain 'B' and resid 108 through 126 Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.535A pdb=" N GLU B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 200 removed outlier: 3.585A pdb=" N ILE B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 225 through 245 removed outlier: 3.963A pdb=" N LYS B 230 " --> pdb=" O PRO B 226 " (cutoff:3.500A) Proline residue: B 231 - end of helix removed outlier: 3.514A pdb=" N ARG B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 81 through 104 removed outlier: 3.678A pdb=" N VAL C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 126 removed outlier: 3.568A pdb=" N TYR C 123 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.976A pdb=" N LYS C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 200 Processing helix chain 'C' and resid 225 through 244 Proline residue: C 231 - end of helix removed outlier: 3.537A pdb=" N ARG C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 3.626A 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 104 Processing helix chain 'D' and resid 108 through 126 Processing helix chain 'D' and resid 167 through 179 Processing helix chain 'D' and resid 184 through 200 removed outlier: 3.627A pdb=" N ILE D 200 " --> pdb=" O MET D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 244 removed outlier: 4.004A pdb=" N LYS D 230 " --> pdb=" O PRO D 226 " (cutoff:3.500A) 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: 3.667A pdb=" N GLU D 238 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.691A pdb=" N GLY E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 104 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.761A pdb=" N ALA E 113 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR E 123 " --> pdb=" O PHE E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 179 Processing helix chain 'E' and resid 184 through 201 removed outlier: 3.563A pdb=" N SER E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE E 200 " --> pdb=" O MET E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 244 Proline residue: E 231 - end of helix removed outlier: 3.668A pdb=" N GLU E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG E 239 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 33 Processing helix chain 'F' and resid 81 through 104 removed outlier: 3.727A pdb=" N ARG F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 123 removed outlier: 3.544A pdb=" N TYR F 123 " --> pdb=" O PHE F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 179 removed outlier: 3.688A pdb=" N LYS F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 201 Processing helix chain 'F' and resid 205 through 207 No H-bonds generated for 'chain 'F' and resid 205 through 207' Processing helix chain 'F' and resid 225 through 243 Proline residue: F 231 - end of helix removed outlier: 3.802A pdb=" N GLU F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG F 239 " --> pdb=" O ARG F 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.623A pdb=" N TYR G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.659A pdb=" N LYS G 177 " --> pdb=" O GLU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 201 removed outlier: 3.545A pdb=" N ILE G 200 " --> pdb=" O MET G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 244 Proline residue: G 231 - end of helix removed outlier: 3.621A pdb=" N GLU G 238 " --> pdb=" O GLU G 234 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG G 239 " --> pdb=" O ARG G 235 " (cutoff:3.500A) Processing helix chain '1' and resid 60 through 82 Processing helix chain '1' and resid 86 through 101 Processing helix chain '1' and resid 143 through 155 removed outlier: 4.175A pdb=" N GLY 1 149 " --> pdb=" O LEU 1 145 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL 1 150 " --> pdb=" O THR 1 146 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP 1 153 " --> pdb=" O GLY 1 149 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG 1 154 " --> pdb=" O VAL 1 150 " (cutoff:3.500A) Processing helix chain '1' and resid 160 through 177 removed outlier: 4.247A pdb=" N GLU 1 166 " --> pdb=" O ASP 1 162 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU 1 167 " --> pdb=" O GLU 1 163 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA 1 175 " --> pdb=" O ALA 1 171 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET 1 176 " --> pdb=" O ILE 1 172 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS 1 177 " --> pdb=" O TYR 1 173 " (cutoff:3.500A) Processing helix chain '1' and resid 199 through 206 removed outlier: 4.485A pdb=" N GLU 1 203 " --> pdb=" O TYR 1 199 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 1 204 " --> pdb=" O SER 1 200 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN 1 206 " --> pdb=" O GLU 1 202 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 82 removed outlier: 3.775A pdb=" N ALA 2 63 " --> pdb=" O SER 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 86 through 101 Processing helix chain '2' and resid 143 through 155 removed outlier: 4.215A pdb=" N GLY 2 149 " --> pdb=" O LEU 2 145 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG 2 154 " --> pdb=" O VAL 2 150 " (cutoff:3.500A) Processing helix chain '2' and resid 163 through 179 removed outlier: 4.194A pdb=" N ARG 2 178 " --> pdb=" O SER 2 174 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP 2 179 " --> pdb=" O ALA 2 175 " (cutoff:3.500A) Processing helix chain '2' and resid 199 through 208 removed outlier: 4.511A pdb=" N GLU 2 203 " --> pdb=" O TYR 2 199 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL 2 204 " --> pdb=" O SER 2 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN 2 206 " --> pdb=" O GLU 2 202 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE 2 207 " --> pdb=" O GLU 2 203 " (cutoff:3.500A) Processing helix chain '3' and resid 59 through 82 Processing helix chain '3' and resid 86 through 101 removed outlier: 3.564A pdb=" N ASN 3 99 " --> pdb=" O SER 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 143 through 155 removed outlier: 3.798A pdb=" N GLY 3 149 " --> pdb=" O LEU 3 145 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG 3 154 " --> pdb=" O VAL 3 150 " (cutoff:3.500A) Processing helix chain '3' and resid 160 through 177 Processing helix chain '3' and resid 200 through 212 removed outlier: 3.501A pdb=" N GLN 3 206 " --> pdb=" O GLU 3 202 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE 3 207 " --> pdb=" O GLU 3 203 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS 3 210 " --> pdb=" O GLN 3 206 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE 3 211 " --> pdb=" O ILE 3 207 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG 3 212 " --> pdb=" O LEU 3 208 " (cutoff:3.500A) Processing helix chain '4' and resid 59 through 82 removed outlier: 4.239A pdb=" N ALA 4 63 " --> pdb=" O SER 4 59 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN 4 64 " --> pdb=" O VAL 4 60 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE 4 65 " --> pdb=" O GLY 4 61 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU 4 66 " --> pdb=" O ASP 4 62 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG 4 68 " --> pdb=" O GLN 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 86 through 101 removed outlier: 3.566A pdb=" N ILE 4 90 " --> pdb=" O THR 4 86 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR 4 101 " --> pdb=" O LEU 4 97 " (cutoff:3.500A) Processing helix chain '4' and resid 143 through 152 Processing helix chain '4' and resid 160 through 179 removed outlier: 3.549A pdb=" N LYS 4 177 " --> pdb=" O TYR 4 173 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG 4 178 " --> pdb=" O SER 4 174 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP 4 179 " --> pdb=" O ALA 4 175 " (cutoff:3.500A) Processing helix chain '4' and resid 199 through 205 removed outlier: 3.826A pdb=" N GLU 4 203 " --> pdb=" O TYR 4 199 " (cutoff:3.500A) Processing helix chain '4' and resid 206 through 208 No H-bonds generated for 'chain '4' and resid 206 through 208' Processing helix chain '5' and resid 59 through 82 Processing helix chain '5' and resid 86 through 101 Processing helix chain '5' and resid 143 through 155 removed outlier: 3.981A pdb=" N ARG 5 154 " --> pdb=" O VAL 5 150 " (cutoff:3.500A) Processing helix chain '5' and resid 160 through 177 removed outlier: 3.776A pdb=" N ALA 5 175 " --> pdb=" O ALA 5 171 " (cutoff:3.500A) Processing helix chain '5' and resid 200 through 206 removed outlier: 3.830A pdb=" N GLN 5 206 " --> pdb=" O GLU 5 202 " (cutoff:3.500A) Processing helix chain '6' and resid 59 through 82 removed outlier: 3.537A pdb=" N ALA 6 63 " --> pdb=" O SER 6 59 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG 6 68 " --> pdb=" O GLN 6 64 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE 6 69 " --> pdb=" O PHE 6 65 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 101 removed outlier: 3.532A pdb=" N ALA 6 91 " --> pdb=" O VAL 6 87 " (cutoff:3.500A) Processing helix chain '6' and resid 102 through 104 No H-bonds generated for 'chain '6' and resid 102 through 104' Processing helix chain '6' and resid 143 through 155 removed outlier: 4.120A pdb=" N ASP 6 153 " --> pdb=" O GLY 6 149 " (cutoff:3.500A) Processing helix chain '6' and resid 160 through 179 removed outlier: 3.537A pdb=" N LYS 6 177 " --> pdb=" O TYR 6 173 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 208 removed outlier: 4.090A pdb=" N GLU 6 203 " --> pdb=" O TYR 6 199 " (cutoff:3.500A) Processing helix chain '7' and resid 59 through 82 removed outlier: 3.588A pdb=" N ALA 7 63 " --> pdb=" O SER 7 59 " (cutoff:3.500A) Processing helix chain '7' and resid 86 through 101 Processing helix chain '7' and resid 143 through 155 removed outlier: 3.595A pdb=" N ASP 7 153 " --> pdb=" O GLY 7 149 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG 7 154 " --> pdb=" O VAL 7 150 " (cutoff:3.500A) Processing helix chain '7' and resid 160 through 176 removed outlier: 3.514A pdb=" N ALA 7 175 " --> pdb=" O ALA 7 171 " (cutoff:3.500A) Processing helix chain '7' and resid 199 through 208 removed outlier: 4.415A pdb=" N GLU 7 203 " --> pdb=" O TYR 7 199 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL 7 204 " --> pdb=" O SER 7 200 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE 7 207 " --> pdb=" O GLU 7 203 " (cutoff:3.500A) Processing helix chain '7' and resid 209 through 211 No H-bonds generated for 'chain '7' and resid 209 through 211' Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 164 removed outlier: 3.885A pdb=" N GLY A 45 " --> pdb=" O CYS A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 71 removed outlier: 6.878A pdb=" N ILE A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.720A pdb=" N GLY B 45 " --> pdb=" O CYS B 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 removed outlier: 3.674A pdb=" N ALA B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.767A 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: 3.984A pdb=" N LEU C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 161 through 164 removed outlier: 3.567A pdb=" N GLY D 45 " --> pdb=" O CYS D 42 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 220 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 71 removed outlier: 7.343A pdb=" N ILE D 67 " --> pdb=" O THR D 78 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N THR D 78 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LYS D 69 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA D 76 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU D 136 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU D 147 " --> pdb=" O TYR D 159 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP D 151 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 161 through 164 removed outlier: 4.205A pdb=" N LYS E 215 " --> pdb=" O THR E 220 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR E 220 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.465A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 136 " --> pdb=" O THR E 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 161 through 164 removed outlier: 3.599A pdb=" N ALA F 37 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS F 222 " --> pdb=" O TYR F 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 69 removed outlier: 3.995A pdb=" N LEU F 136 " --> pdb=" O THR F 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 161 through 162 removed outlier: 4.175A pdb=" N VAL G 211 " --> pdb=" O VAL G 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 68 through 71 removed outlier: 6.539A pdb=" N ILE G 74 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU G 136 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU G 147 " --> pdb=" O TYR G 159 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU G 157 " --> pdb=" O GLU G 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '1' and resid 137 through 141 removed outlier: 3.669A pdb=" N GLY 1 22 " --> pdb=" O CYS 1 19 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '1' and resid 45 through 49 removed outlier: 6.525A pdb=" N MET 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY 1 113 " --> pdb=" O ALA 1 53 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU 1 110 " --> pdb=" O ILE 1 125 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE 1 122 " --> pdb=" O GLU 1 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 14 through 18 Processing sheet with id=AB9, first strand: chain '2' and resid 31 through 32 removed outlier: 3.945A pdb=" N ALA 2 31 " --> pdb=" O SER 2 39 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER 2 39 " --> pdb=" O ALA 2 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain '2' and resid 45 through 49 removed outlier: 6.948A pdb=" N MET 2 52 " --> pdb=" O ILE 2 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '3' and resid 14 through 18 Processing sheet with id=AC3, first strand: chain '3' and resid 45 through 49 removed outlier: 6.531A pdb=" N MET 3 52 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER 3 121 " --> pdb=" O GLY 3 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE 3 122 " --> pdb=" O GLU 3 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '4' and resid 137 through 138 removed outlier: 3.525A pdb=" N ALA 4 26 " --> pdb=" O VAL 4 15 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '4' and resid 45 through 49 removed outlier: 6.625A pdb=" N MET 4 52 " --> pdb=" O ILE 4 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER 4 121 " --> pdb=" O GLY 4 114 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE 4 122 " --> pdb=" O GLU 4 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 137 through 141 removed outlier: 6.543A pdb=" N THR 5 13 " --> pdb=" O GLU 5 28 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU 5 28 " --> pdb=" O THR 5 13 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET 5 25 " --> pdb=" O VAL 5 189 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 45 through 49 removed outlier: 6.794A pdb=" N MET 5 52 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE 5 122 " --> pdb=" O GLU 5 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '6' and resid 137 through 138 Processing sheet with id=AC9, first strand: chain '6' and resid 45 through 49 removed outlier: 6.454A pdb=" N MET 6 52 " --> pdb=" O ILE 6 48 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE 6 122 " --> pdb=" O GLU 6 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '7' and resid 137 through 138 Processing sheet with id=AD2, first strand: chain '7' and resid 32 through 33 removed outlier: 3.507A pdb=" N PHE 7 36 " --> pdb=" O MET 7 33 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '7' and resid 45 through 49 removed outlier: 6.836A pdb=" N MET 7 52 " --> pdb=" O ILE 7 48 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE 7 132 " --> pdb=" O SER 7 124 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP 7 126 " --> pdb=" O GLY 7 130 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLY 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) 1337 hydrogen bonds defined for protein. 3924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.37 Time building geometry restraints manager: 8.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.52: 17623 1.52 - 1.88: 6505 1.88 - 2.24: 13 2.24 - 2.61: 1 2.61 - 2.97: 1 Bond restraints: 24143 Sorted by residual: bond pdb=" CG PHE 5 211 " pdb=" CD2 PHE 5 211 " ideal model delta sigma weight residual 1.384 2.968 -1.584 2.10e-02 2.27e+03 5.69e+03 bond pdb=" CG PHE 5 211 " pdb=" CD1 PHE 5 211 " ideal model delta sigma weight residual 1.384 2.182 -0.798 2.10e-02 2.27e+03 1.44e+03 bond pdb=" CE1 PHE 5 211 " pdb=" CZ PHE 5 211 " ideal model delta sigma weight residual 1.382 2.264 -0.882 3.00e-02 1.11e+03 8.64e+02 bond pdb=" CD2 PHE 5 211 " pdb=" CE2 PHE 5 211 " ideal model delta sigma weight residual 1.382 2.225 -0.843 3.00e-02 1.11e+03 7.89e+02 bond pdb=" CE2 PHE 5 211 " pdb=" CZ PHE 5 211 " ideal model delta sigma weight residual 1.382 2.200 -0.818 3.00e-02 1.11e+03 7.44e+02 ... (remaining 24138 not shown) Histogram of bond angle deviations from ideal: 84.84 - 101.16: 307 101.16 - 117.47: 17681 117.47 - 133.79: 14568 133.79 - 150.10: 14 150.10 - 166.42: 1 Bond angle restraints: 32571 Sorted by residual: angle pdb=" O ASP C 181 " pdb=" C ASP C 181 " pdb=" N ASP C 182 " ideal model delta sigma weight residual 122.59 166.42 -43.83 1.33e+00 5.65e-01 1.09e+03 angle pdb=" CA ASP C 181 " pdb=" C ASP C 181 " pdb=" O ASP C 181 " ideal model delta sigma weight residual 120.51 84.84 35.67 1.43e+00 4.89e-01 6.22e+02 angle pdb=" CA ASP C 181 " pdb=" C ASP C 181 " pdb=" N ASP C 182 " ideal model delta sigma weight residual 116.84 84.96 31.88 1.71e+00 3.42e-01 3.48e+02 angle pdb=" N ASP C 182 " pdb=" CA ASP C 182 " pdb=" CB ASP C 182 " ideal model delta sigma weight residual 110.56 133.77 -23.21 1.86e+00 2.89e-01 1.56e+02 angle pdb=" N LYS A 66 " pdb=" CA LYS A 66 " pdb=" C LYS A 66 " ideal model delta sigma weight residual 114.62 100.61 14.01 1.14e+00 7.69e-01 1.51e+02 ... (remaining 32566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.74: 13908 24.74 - 49.48: 657 49.48 - 74.21: 203 74.21 - 98.95: 78 98.95 - 123.69: 1 Dihedral angle restraints: 14847 sinusoidal: 5992 harmonic: 8855 Sorted by residual: dihedral pdb=" CA VAL G 54 " pdb=" C VAL G 54 " pdb=" N GLY G 55 " pdb=" CA GLY G 55 " ideal model delta harmonic sigma weight residual 180.00 56.31 123.69 0 5.00e+00 4.00e-02 6.12e+02 dihedral pdb=" CA ARG G 53 " pdb=" C ARG G 53 " pdb=" N VAL G 54 " pdb=" CA VAL G 54 " ideal model delta harmonic sigma weight residual 180.00 112.64 67.36 0 5.00e+00 4.00e-02 1.81e+02 dihedral pdb=" CA LYS G 52 " pdb=" C LYS G 52 " pdb=" N ARG G 53 " pdb=" CA ARG G 53 " ideal model delta harmonic sigma weight residual 180.00 -117.93 -62.07 0 5.00e+00 4.00e-02 1.54e+02 ... (remaining 14844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 2343 0.180 - 0.360: 1110 0.360 - 0.539: 289 0.539 - 0.719: 27 0.719 - 0.899: 4 Chirality restraints: 3773 Sorted by residual: chirality pdb=" CA THR 6 140 " pdb=" N THR 6 140 " pdb=" C THR 6 140 " pdb=" CB THR 6 140 " both_signs ideal model delta sigma weight residual False 2.53 1.63 0.90 2.00e-01 2.50e+01 2.02e+01 chirality pdb=" CA LEU 2 208 " pdb=" N LEU 2 208 " pdb=" C LEU 2 208 " pdb=" CB LEU 2 208 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" CA ARG D 219 " pdb=" N ARG D 219 " pdb=" C ARG D 219 " pdb=" CB ARG D 219 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 3770 not shown) Planarity restraints: 4193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 4 103 " -0.240 2.00e-02 2.50e+03 1.63e-01 5.32e+02 pdb=" CG TYR 4 103 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR 4 103 " 0.065 2.00e-02 2.50e+03 pdb=" CD2 TYR 4 103 " 0.084 2.00e-02 2.50e+03 pdb=" CE1 TYR 4 103 " 0.195 2.00e-02 2.50e+03 pdb=" CE2 TYR 4 103 " 0.147 2.00e-02 2.50e+03 pdb=" CZ TYR 4 103 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR 4 103 " -0.289 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 1 197 " 0.315 2.00e-02 2.50e+03 1.62e-01 5.25e+02 pdb=" CG TYR 1 197 " -0.102 2.00e-02 2.50e+03 pdb=" CD1 TYR 1 197 " -0.190 2.00e-02 2.50e+03 pdb=" CD2 TYR 1 197 " -0.129 2.00e-02 2.50e+03 pdb=" CE1 TYR 1 197 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR 1 197 " -0.068 2.00e-02 2.50e+03 pdb=" CZ TYR 1 197 " 0.023 2.00e-02 2.50e+03 pdb=" OH TYR 1 197 " 0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 5 211 " 0.115 2.00e-02 2.50e+03 1.71e-01 5.10e+02 pdb=" CG PHE 5 211 " -0.112 2.00e-02 2.50e+03 pdb=" CD1 PHE 5 211 " 0.083 2.00e-02 2.50e+03 pdb=" CD2 PHE 5 211 " -0.228 2.00e-02 2.50e+03 pdb=" CE1 PHE 5 211 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 PHE 5 211 " 0.320 2.00e-02 2.50e+03 pdb=" CZ PHE 5 211 " -0.114 2.00e-02 2.50e+03 ... (remaining 4190 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 961 2.64 - 3.21: 19098 3.21 - 3.77: 36443 3.77 - 4.34: 52672 4.34 - 4.90: 85789 Nonbonded interactions: 194963 Sorted by model distance: nonbonded pdb=" NH1 ARG 5 170 " pdb=" CD2 PHE 5 211 " model vdw 2.081 3.420 nonbonded pdb=" NE ARG 5 170 " pdb=" CD1 PHE 5 211 " model vdw 2.159 3.420 nonbonded pdb=" OE1 GLU 5 166 " pdb=" CE2 PHE 5 211 " model vdw 2.184 3.340 nonbonded pdb=" CZ ARG 5 170 " pdb=" CE2 PHE 5 211 " model vdw 2.192 3.570 nonbonded pdb=" NH1 ARG 5 170 " pdb=" CG PHE 5 211 " model vdw 2.206 3.340 ... (remaining 194958 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' } 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.480 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 57.390 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.150 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 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 : 0.039 1.584 24143 Z= 2.505 Angle : 3.601 43.828 32571 Z= 2.410 Chirality : 0.206 0.899 3773 Planarity : 0.030 0.298 4193 Dihedral : 17.647 123.688 9177 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 1.55 % Allowed : 5.58 % Favored : 92.87 % Rotamer: Outliers : 4.93 % Allowed : 10.89 % Favored : 84.18 % Cbeta Deviations : 7.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.74 % 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: -2.44 (0.13), residues: 3031 helix: -0.35 (0.13), residues: 1211 sheet: -1.06 (0.18), residues: 620 loop : -3.29 (0.12), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.035 0.011 HIS C 73 PHE 0.320 0.039 PHE 5 211 TYR 0.315 0.050 TYR 1 197 ARG 0.084 0.012 ARG 3 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 669 time to evaluate : 2.496 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: B 141 VAL cc_start: 0.9124 (t) cc_final: 0.8870 (m) REVERT: C 104 ASP cc_start: 0.8250 (t70) cc_final: 0.7989 (t0) REVERT: C 141 VAL cc_start: 0.9226 (t) cc_final: 0.8984 (m) REVERT: D 111 GLU cc_start: 0.7408 (tp30) cc_final: 0.6757 (tp30) REVERT: D 129 VAL cc_start: 0.8767 (p) cc_final: 0.8474 (m) REVERT: D 203 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6856 (mt-10) REVERT: G 71 ASP cc_start: 0.7580 (t0) cc_final: 0.6916 (t0) REVERT: G 159 TYR cc_start: 0.8344 (m-80) cc_final: 0.8034 (m-80) REVERT: G 196 MET cc_start: 0.7652 (ttm) cc_final: 0.7358 (ttm) REVERT: 1 128 ILE cc_start: 0.3763 (OUTLIER) cc_final: 0.3506 (tt) REVERT: 2 72 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.7783 (mp) REVERT: 3 39 SER cc_start: 0.3347 (OUTLIER) cc_final: 0.2804 (t) REVERT: 3 40 LYS cc_start: 0.3887 (OUTLIER) cc_final: 0.2321 (tppt) REVERT: 3 137 ILE cc_start: 0.6151 (OUTLIER) cc_final: 0.5916 (mm) REVERT: 4 71 LYS cc_start: 0.8276 (tttt) cc_final: 0.8000 (tttm) REVERT: 4 88 ARG cc_start: 0.7170 (ttp-110) cc_final: 0.6890 (ttm-80) REVERT: 4 134 GLU cc_start: 0.7099 (mp0) cc_final: 0.6898 (mp0) REVERT: 5 33 MET cc_start: -0.0386 (mtp) cc_final: -0.2142 (ppp) REVERT: 6 123 TYR cc_start: 0.8062 (m-80) cc_final: 0.7561 (m-80) REVERT: 7 84 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8688 (mmmm) REVERT: 7 205 GLU cc_start: 0.6115 (OUTLIER) cc_final: 0.4948 (mp0) outliers start: 125 outliers final: 29 residues processed: 762 average time/residue: 0.4185 time to fit residues: 461.1018 Evaluate side-chains 560 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 525 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain 1 residue 72 ILE Chi-restraints excluded: chain 1 residue 128 ILE Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 72 ILE Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 3 residue 39 SER Chi-restraints excluded: chain 3 residue 40 LYS Chi-restraints excluded: chain 3 residue 125 ILE Chi-restraints excluded: chain 3 residue 137 ILE Chi-restraints excluded: chain 4 residue 72 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 150 VAL Chi-restraints excluded: chain 5 residue 205 GLU Chi-restraints excluded: chain 6 residue 14 THR Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 105 PRO Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 103 TYR Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 254 optimal weight: 0.9990 chunk 228 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 153 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 235 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 175 optimal weight: 0.5980 chunk 273 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN D 23 GLN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN E 237 ASN G 73 HIS G 237 ASN 1 96 ASN 1 198 GLN 3 96 ASN 6 47 GLN 6 64 GLN 6 96 ASN 7 75 ASN 7 96 ASN 7 198 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.849 24143 Z= 0.970 Angle : 0.819 30.795 32571 Z= 0.452 Chirality : 0.050 0.267 3773 Planarity : 0.006 0.073 4193 Dihedral : 7.743 84.939 3457 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.04 % Favored : 96.80 % Rotamer: Outliers : 3.67 % Allowed : 15.94 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.98 (0.14), residues: 3031 helix: 0.82 (0.14), residues: 1253 sheet: -0.61 (0.18), residues: 652 loop : -2.39 (0.15), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 73 PHE 0.034 0.002 PHE 5 211 TYR 0.025 0.002 TYR E 213 ARG 0.014 0.001 ARG 5 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 536 time to evaluate : 2.700 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: A 66 LYS cc_start: 0.8003 (mmmt) cc_final: 0.7663 (mmtp) REVERT: A 228 GLU cc_start: 0.7506 (tt0) cc_final: 0.7252 (tt0) REVERT: B 205 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.8011 (m) REVERT: B 239 ARG cc_start: 0.7566 (tpt170) cc_final: 0.7021 (tpt170) REVERT: C 95 GLU cc_start: 0.8281 (tp30) cc_final: 0.7832 (tp30) REVERT: C 104 ASP cc_start: 0.8182 (t70) cc_final: 0.7942 (t70) REVERT: E 71 ASP cc_start: 0.7687 (t0) cc_final: 0.7419 (t0) REVERT: E 159 TYR cc_start: 0.8808 (m-80) cc_final: 0.8565 (m-80) REVERT: 1 84 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8186 (mtpp) REVERT: 2 17 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7689 (pt) REVERT: 2 88 ARG cc_start: 0.7237 (ttm-80) cc_final: 0.7033 (ttm-80) REVERT: 2 155 PHE cc_start: 0.7258 (t80) cc_final: 0.6965 (t80) REVERT: 3 106 TYR cc_start: 0.3249 (OUTLIER) cc_final: 0.1991 (t80) REVERT: 4 33 MET cc_start: -0.1046 (OUTLIER) cc_final: -0.1443 (mtm) REVERT: 4 51 ARG cc_start: 0.7536 (mmp80) cc_final: 0.7252 (mmp80) REVERT: 4 90 ILE cc_start: 0.8862 (mm) cc_final: 0.8633 (mm) REVERT: 4 134 GLU cc_start: 0.7631 (mp0) cc_final: 0.6934 (mp0) REVERT: 7 44 LYS cc_start: 0.8261 (tppt) cc_final: 0.7982 (tptp) REVERT: 7 205 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.4564 (mp0) outliers start: 93 outliers final: 50 residues processed: 592 average time/residue: 0.3948 time to fit residues: 351.4586 Evaluate side-chains 511 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 456 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 121 SER Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 194 ASP Chi-restraints excluded: chain 4 residue 33 MET Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 187 ASP Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 136 ASP Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 151 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 227 optimal weight: 0.6980 chunk 186 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 273 optimal weight: 0.9980 chunk 295 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 271 optimal weight: 0.0970 chunk 93 optimal weight: 0.9980 chunk 219 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 HIS G 169 ASN 4 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.900 24143 Z= 0.962 Angle : 0.714 29.929 32571 Z= 0.390 Chirality : 0.047 0.206 3773 Planarity : 0.005 0.074 4193 Dihedral : 6.513 86.662 3416 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.00 % Favored : 96.83 % Rotamer: Outliers : 4.03 % Allowed : 17.76 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3031 helix: 0.98 (0.14), residues: 1250 sheet: -0.42 (0.19), residues: 646 loop : -2.00 (0.15), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 73 PHE 0.029 0.002 PHE 3 211 TYR 0.022 0.002 TYR G 213 ARG 0.012 0.001 ARG 3 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 465 time to evaluate : 2.880 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: A 66 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7715 (mmtp) REVERT: B 205 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7851 (m) REVERT: B 239 ARG cc_start: 0.7561 (tpt170) cc_final: 0.7270 (tpt170) REVERT: C 95 GLU cc_start: 0.8190 (tp30) cc_final: 0.7780 (tp30) REVERT: C 223 GLU cc_start: 0.6695 (tt0) cc_final: 0.6443 (tt0) REVERT: D 129 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8735 (m) REVERT: E 22 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.7311 (m-10) REVERT: E 71 ASP cc_start: 0.7908 (t0) cc_final: 0.7590 (t0) REVERT: E 222 LYS cc_start: 0.8169 (ptmt) cc_final: 0.7949 (ptmt) REVERT: F 121 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7808 (tm-30) REVERT: G 196 MET cc_start: 0.8271 (tpp) cc_final: 0.7878 (tpp) REVERT: G 242 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7424 (tm-30) REVERT: 1 84 LYS cc_start: 0.8384 (ttmm) cc_final: 0.8117 (mtpp) REVERT: 2 163 GLU cc_start: 0.6390 (pm20) cc_final: 0.6115 (pm20) REVERT: 3 106 TYR cc_start: 0.3419 (OUTLIER) cc_final: 0.2044 (t80) REVERT: 4 88 ARG cc_start: 0.7638 (ttp80) cc_final: 0.7259 (ttm-80) REVERT: 6 134 GLU cc_start: 0.7996 (mp0) cc_final: 0.7712 (mm-30) REVERT: 7 187 ASP cc_start: 0.6101 (p0) cc_final: 0.5825 (p0) REVERT: 7 205 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.5277 (mp0) outliers start: 102 outliers final: 65 residues processed: 529 average time/residue: 0.3688 time to fit residues: 296.9548 Evaluate side-chains 490 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 420 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 72 ILE Chi-restraints excluded: chain 2 residue 75 ASN Chi-restraints excluded: chain 2 residue 121 SER Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 5 residue 154 ARG Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 187 ASP Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 136 ASP Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 270 optimal weight: 0.0050 chunk 205 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 130 optimal weight: 0.5980 chunk 183 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 290 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 260 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN C 99 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.905 24143 Z= 0.943 Angle : 0.650 29.672 32571 Z= 0.355 Chirality : 0.045 0.209 3773 Planarity : 0.004 0.068 4193 Dihedral : 6.072 88.126 3410 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.84 % Favored : 97.00 % Rotamer: Outliers : 3.79 % Allowed : 19.06 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3031 helix: 1.10 (0.15), residues: 1259 sheet: -0.22 (0.19), residues: 635 loop : -1.77 (0.16), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 73 PHE 0.025 0.001 PHE 5 211 TYR 0.019 0.001 TYR 5 173 ARG 0.017 0.001 ARG 5 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 438 time to evaluate : 2.384 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: A 66 LYS cc_start: 0.8000 (mmmt) cc_final: 0.7670 (mmtp) REVERT: B 205 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7719 (m) REVERT: B 239 ARG cc_start: 0.7490 (tpt170) cc_final: 0.7154 (tpt170) REVERT: C 95 GLU cc_start: 0.8116 (tp30) cc_final: 0.7673 (tp30) REVERT: D 129 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8696 (m) REVERT: E 71 ASP cc_start: 0.7910 (t0) cc_final: 0.7592 (t0) REVERT: G 242 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7229 (tm-30) REVERT: 1 84 LYS cc_start: 0.8354 (ttmm) cc_final: 0.8141 (mtpp) REVERT: 1 152 GLU cc_start: 0.5505 (mt-10) cc_final: 0.5183 (mt-10) REVERT: 2 56 THR cc_start: 0.7476 (OUTLIER) cc_final: 0.7198 (m) REVERT: 3 106 TYR cc_start: 0.3245 (OUTLIER) cc_final: 0.1790 (t80) REVERT: 4 88 ARG cc_start: 0.7527 (ttp80) cc_final: 0.7270 (ttm-80) REVERT: 4 191 ILE cc_start: 0.8899 (mp) cc_final: 0.8612 (mt) REVERT: 5 110 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8593 (mt) REVERT: 6 134 GLU cc_start: 0.7874 (mp0) cc_final: 0.7484 (mm-30) REVERT: 7 44 LYS cc_start: 0.8227 (tppt) cc_final: 0.7626 (tptp) REVERT: 7 205 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.5436 (mp0) outliers start: 96 outliers final: 64 residues processed: 502 average time/residue: 0.3638 time to fit residues: 279.1174 Evaluate side-chains 484 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 414 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 56 THR Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 187 ASP Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 55 THR Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 5 residue 154 ARG Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 82 GLU Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 187 ASP Chi-restraints excluded: chain 6 residue 193 GLU Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 242 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN 5 198 GLN 7 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.907 24143 Z= 0.988 Angle : 0.716 29.470 32571 Z= 0.385 Chirality : 0.048 0.183 3773 Planarity : 0.005 0.075 4193 Dihedral : 5.955 87.362 3402 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.34 % Rotamer: Outliers : 5.05 % Allowed : 19.34 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3031 helix: 0.87 (0.14), residues: 1251 sheet: -0.32 (0.19), residues: 653 loop : -1.70 (0.16), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 73 PHE 0.026 0.002 PHE 5 211 TYR 0.020 0.002 TYR D 213 ARG 0.019 0.001 ARG 5 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 475 time to evaluate : 2.675 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: A 66 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7721 (mmtp) REVERT: A 196 MET cc_start: 0.7639 (tpp) cc_final: 0.7281 (tpp) REVERT: B 104 ASP cc_start: 0.8174 (t0) cc_final: 0.7971 (t70) REVERT: B 205 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7832 (m) REVERT: C 95 GLU cc_start: 0.8230 (tp30) cc_final: 0.7752 (tp30) REVERT: E 71 ASP cc_start: 0.8087 (t0) cc_final: 0.7735 (t0) REVERT: 1 25 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7264 (ttp) REVERT: 2 54 MET cc_start: 0.8671 (tmm) cc_final: 0.8358 (ttt) REVERT: 3 106 TYR cc_start: 0.3224 (OUTLIER) cc_final: 0.1361 (t80) REVERT: 4 158 GLU cc_start: 0.6606 (tp30) cc_final: 0.6355 (tp30) REVERT: 5 110 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8727 (mt) REVERT: 6 134 GLU cc_start: 0.8000 (mp0) cc_final: 0.7750 (mm-30) REVERT: 7 44 LYS cc_start: 0.8339 (tppt) cc_final: 0.7916 (tppp) REVERT: 7 205 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5303 (mp0) outliers start: 128 outliers final: 91 residues processed: 558 average time/residue: 0.3700 time to fit residues: 317.8320 Evaluate side-chains 540 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 444 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 25 MET Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 1 residue 182 SER Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 56 THR Chi-restraints excluded: chain 2 residue 75 ASN Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 118 GLU Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 200 SER Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 136 ASP Chi-restraints excluded: chain 4 residue 187 ASP Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 33 MET Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 55 THR Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 161 VAL Chi-restraints excluded: chain 7 residue 83 ARG Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 136 ASP Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 97 optimal weight: 0.0010 chunk 262 optimal weight: 0.8980 chunk 57 optimal weight: 0.0970 chunk 170 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 291 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 134 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 overall best weight: 0.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN D 122 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.908 24143 Z= 0.940 Angle : 0.635 29.320 32571 Z= 0.344 Chirality : 0.045 0.266 3773 Planarity : 0.004 0.084 4193 Dihedral : 5.679 86.376 3402 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.03 % Rotamer: Outliers : 3.67 % Allowed : 21.78 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3031 helix: 1.18 (0.15), residues: 1240 sheet: -0.22 (0.19), residues: 646 loop : -1.62 (0.16), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS G 73 PHE 0.026 0.001 PHE 5 211 TYR 0.014 0.001 TYR D 213 ARG 0.020 0.000 ARG 5 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 432 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7716 (mmtp) REVERT: A 159 TYR cc_start: 0.8774 (m-80) cc_final: 0.8507 (m-80) REVERT: B 104 ASP cc_start: 0.8019 (t0) cc_final: 0.7405 (t0) REVERT: B 205 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7811 (m) REVERT: C 95 GLU cc_start: 0.8091 (tp30) cc_final: 0.7676 (tp30) REVERT: E 71 ASP cc_start: 0.8096 (t0) cc_final: 0.7787 (t0) REVERT: 1 25 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7322 (ttp) REVERT: 2 54 MET cc_start: 0.8718 (tmm) cc_final: 0.8347 (ttt) REVERT: 2 84 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8118 (mmmm) REVERT: 2 120 LYS cc_start: 0.7841 (mptt) cc_final: 0.7497 (mptt) REVERT: 3 106 TYR cc_start: 0.3044 (OUTLIER) cc_final: 0.1094 (t80) REVERT: 4 51 ARG cc_start: 0.7871 (mmt-90) cc_final: 0.7543 (mmp80) REVERT: 5 110 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8674 (mt) REVERT: 6 29 LYS cc_start: 0.7242 (mttt) cc_final: 0.7028 (mttm) REVERT: 6 134 GLU cc_start: 0.7894 (mp0) cc_final: 0.7460 (mm-30) REVERT: 6 152 GLU cc_start: 0.5990 (mt-10) cc_final: 0.5747 (mt-10) REVERT: 7 44 LYS cc_start: 0.8305 (tppt) cc_final: 0.7849 (tptp) REVERT: 7 205 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.5302 (mp0) outliers start: 93 outliers final: 68 residues processed: 495 average time/residue: 0.3669 time to fit residues: 277.5424 Evaluate side-chains 487 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 414 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 25 MET Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 118 GLU Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 187 ASP Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 33 MET Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 161 VAL Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 136 ASP Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 280 optimal weight: 0.0060 chunk 32 optimal weight: 0.2980 chunk 165 optimal weight: 0.9990 chunk 212 optimal weight: 0.1980 chunk 164 optimal weight: 0.4980 chunk 245 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 290 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 176 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.908 24143 Z= 0.940 Angle : 0.622 29.356 32571 Z= 0.336 Chirality : 0.045 0.215 3773 Planarity : 0.004 0.086 4193 Dihedral : 5.536 85.384 3402 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.96 % Rotamer: Outliers : 3.75 % Allowed : 22.06 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3031 helix: 1.26 (0.15), residues: 1242 sheet: -0.16 (0.19), residues: 644 loop : -1.57 (0.16), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 73 PHE 0.026 0.001 PHE 5 211 TYR 0.014 0.001 TYR D 213 ARG 0.021 0.001 ARG 5 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 424 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8171 (mmmt) cc_final: 0.7713 (mmtp) REVERT: A 159 TYR cc_start: 0.8788 (m-80) cc_final: 0.8502 (m-80) REVERT: A 196 MET cc_start: 0.8422 (tpp) cc_final: 0.8074 (tpp) REVERT: B 104 ASP cc_start: 0.7910 (t0) cc_final: 0.7213 (t0) REVERT: B 186 ASP cc_start: 0.7037 (t0) cc_final: 0.6799 (t0) REVERT: B 205 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7793 (m) REVERT: C 95 GLU cc_start: 0.8090 (tp30) cc_final: 0.7683 (tp30) REVERT: E 71 ASP cc_start: 0.8102 (t0) cc_final: 0.7752 (t0) REVERT: 1 25 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7384 (ttp) REVERT: 2 54 MET cc_start: 0.8660 (tmm) cc_final: 0.8381 (ttt) REVERT: 2 84 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8331 (mmmm) REVERT: 2 120 LYS cc_start: 0.7896 (mptt) cc_final: 0.7565 (mptt) REVERT: 3 52 MET cc_start: 0.7654 (mtm) cc_final: 0.7445 (mtp) REVERT: 3 106 TYR cc_start: 0.2999 (OUTLIER) cc_final: 0.0967 (t80) REVERT: 5 55 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.7504 (p) REVERT: 5 110 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8637 (mt) REVERT: 6 134 GLU cc_start: 0.7792 (mp0) cc_final: 0.7224 (mm-30) REVERT: 7 44 LYS cc_start: 0.8322 (tppt) cc_final: 0.7923 (tptp) REVERT: 7 205 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.5201 (mp0) outliers start: 95 outliers final: 76 residues processed: 493 average time/residue: 0.3641 time to fit residues: 275.7945 Evaluate side-chains 488 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 406 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 217 ASP Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 25 MET Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 75 ASN Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 118 GLU Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 55 THR Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 161 VAL Chi-restraints excluded: chain 6 residue 187 ASP Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 136 ASP Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 179 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 173 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 228 optimal weight: 0.6980 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 237 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN F 237 ASN ** 4 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.909 24143 Z= 0.979 Angle : 0.690 29.266 32571 Z= 0.368 Chirality : 0.047 0.215 3773 Planarity : 0.005 0.087 4193 Dihedral : 5.660 84.554 3402 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 4.38 % Allowed : 21.43 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3031 helix: 1.06 (0.15), residues: 1237 sheet: -0.22 (0.19), residues: 641 loop : -1.58 (0.16), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 73 PHE 0.026 0.002 PHE 5 211 TYR 0.020 0.002 TYR D 213 ARG 0.021 0.001 ARG 5 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 411 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 TYR cc_start: 0.8874 (m-80) cc_final: 0.8562 (m-80) REVERT: A 196 MET cc_start: 0.8556 (tpp) cc_final: 0.8147 (tpp) REVERT: B 104 ASP cc_start: 0.8167 (t0) cc_final: 0.7612 (t0) REVERT: B 186 ASP cc_start: 0.7082 (t0) cc_final: 0.6775 (t0) REVERT: B 205 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7828 (m) REVERT: C 38 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8410 (mt) REVERT: C 95 GLU cc_start: 0.8128 (tp30) cc_final: 0.7714 (tp30) REVERT: 2 54 MET cc_start: 0.8770 (tmm) cc_final: 0.8378 (ttt) REVERT: 2 84 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8395 (mmmm) REVERT: 2 120 LYS cc_start: 0.7888 (mptt) cc_final: 0.7596 (mptt) REVERT: 3 106 TYR cc_start: 0.2946 (OUTLIER) cc_final: 0.0805 (t80) REVERT: 4 193 GLU cc_start: 0.6572 (pp20) cc_final: 0.6026 (pp20) REVERT: 5 51 ARG cc_start: 0.7660 (mmp80) cc_final: 0.7430 (mmt180) REVERT: 7 44 LYS cc_start: 0.8402 (tppt) cc_final: 0.8045 (tptp) REVERT: 7 51 ARG cc_start: 0.8421 (mmt-90) cc_final: 0.7560 (mmt180) REVERT: 7 205 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.5260 (mp0) outliers start: 111 outliers final: 88 residues processed: 487 average time/residue: 0.3541 time to fit residues: 267.5020 Evaluate side-chains 492 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 400 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 217 ASP Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 163 GLU Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 75 ASN Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 136 ASP Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 54 MET Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 187 ASP Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 136 ASP Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 263 optimal weight: 5.9990 chunk 277 optimal weight: 0.8980 chunk 253 optimal weight: 0.7980 chunk 270 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 212 optimal weight: 0.0570 chunk 82 optimal weight: 0.3980 chunk 244 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 269 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.908 24143 Z= 0.959 Angle : 0.660 29.250 32571 Z= 0.353 Chirality : 0.046 0.245 3773 Planarity : 0.004 0.088 4193 Dihedral : 5.512 85.915 3400 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 4.03 % Allowed : 22.22 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.24 (0.15), residues: 3031 helix: 1.10 (0.15), residues: 1246 sheet: -0.18 (0.19), residues: 631 loop : -1.53 (0.16), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 73 PHE 0.026 0.001 PHE 5 211 TYR 0.029 0.001 TYR 6 148 ARG 0.022 0.001 ARG 5 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 404 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 TYR cc_start: 0.8863 (m-80) cc_final: 0.8546 (m-80) REVERT: A 196 MET cc_start: 0.8526 (tpp) cc_final: 0.8173 (tpp) REVERT: B 104 ASP cc_start: 0.8074 (t0) cc_final: 0.7446 (t0) REVERT: B 186 ASP cc_start: 0.7027 (t0) cc_final: 0.6721 (t0) REVERT: B 205 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7822 (m) REVERT: C 95 GLU cc_start: 0.8101 (tp30) cc_final: 0.7699 (tp30) REVERT: D 200 ILE cc_start: 0.8069 (pt) cc_final: 0.7858 (pt) REVERT: F 208 ASN cc_start: 0.7949 (p0) cc_final: 0.7703 (p0) REVERT: F 234 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7062 (mm-30) REVERT: G 182 ASP cc_start: 0.7265 (p0) cc_final: 0.7043 (p0) REVERT: 2 54 MET cc_start: 0.8712 (tmm) cc_final: 0.8359 (ttt) REVERT: 2 84 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8416 (mmmm) REVERT: 2 120 LYS cc_start: 0.7886 (mptt) cc_final: 0.7607 (mptt) REVERT: 2 163 GLU cc_start: 0.6877 (pm20) cc_final: 0.6152 (pm20) REVERT: 3 106 TYR cc_start: 0.3566 (OUTLIER) cc_final: 0.1357 (t80) REVERT: 3 118 GLU cc_start: 0.6201 (pt0) cc_final: 0.5490 (pt0) REVERT: 4 134 GLU cc_start: 0.8145 (mp0) cc_final: 0.7941 (mm-30) REVERT: 6 25 MET cc_start: 0.7752 (ttm) cc_final: 0.7421 (ttp) REVERT: 7 44 LYS cc_start: 0.8377 (tppt) cc_final: 0.8034 (tptp) REVERT: 7 51 ARG cc_start: 0.8396 (mmt-90) cc_final: 0.8076 (mmt-90) REVERT: 7 205 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.5208 (mp0) outliers start: 102 outliers final: 90 residues processed: 475 average time/residue: 0.3802 time to fit residues: 283.5133 Evaluate side-chains 499 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 405 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 217 ASP Chi-restraints excluded: chain 1 residue 14 THR Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 163 GLU Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 75 ASN Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 136 ASP Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 14 THR Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 54 MET Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 187 ASP Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 136 ASP Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 177 optimal weight: 0.7980 chunk 285 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 135 optimal weight: 0.0980 chunk 198 optimal weight: 0.8980 chunk 299 optimal weight: 0.6980 chunk 275 optimal weight: 0.0470 chunk 238 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 184 optimal weight: 0.0670 chunk 146 optimal weight: 0.9980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.907 24143 Z= 0.942 Angle : 0.641 29.264 32571 Z= 0.344 Chirality : 0.046 0.287 3773 Planarity : 0.004 0.090 4193 Dihedral : 5.384 86.694 3400 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 3.39 % Allowed : 22.77 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.11 (0.15), residues: 3031 helix: 1.25 (0.15), residues: 1247 sheet: -0.15 (0.19), residues: 631 loop : -1.49 (0.16), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 73 PHE 0.026 0.001 PHE 5 211 TYR 0.012 0.001 TYR G 213 ARG 0.022 0.001 ARG 5 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 411 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8257 (mt) REVERT: A 159 TYR cc_start: 0.8784 (m-80) cc_final: 0.8515 (m-80) REVERT: A 196 MET cc_start: 0.8567 (tpp) cc_final: 0.8209 (tpp) REVERT: B 104 ASP cc_start: 0.7961 (t0) cc_final: 0.7283 (t0) REVERT: B 186 ASP cc_start: 0.7040 (t0) cc_final: 0.6747 (t0) REVERT: B 205 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7739 (m) REVERT: C 95 GLU cc_start: 0.8021 (tp30) cc_final: 0.7640 (tp30) REVERT: D 200 ILE cc_start: 0.8016 (pt) cc_final: 0.7809 (pt) REVERT: F 208 ASN cc_start: 0.7807 (p0) cc_final: 0.7573 (p0) REVERT: F 234 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7117 (mm-30) REVERT: 2 54 MET cc_start: 0.8657 (tmm) cc_final: 0.8354 (ttt) REVERT: 2 84 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8454 (mmmm) REVERT: 2 120 LYS cc_start: 0.7916 (mptt) cc_final: 0.7608 (mptt) REVERT: 3 33 MET cc_start: -0.1293 (ttm) cc_final: -0.1627 (ttm) REVERT: 3 106 TYR cc_start: 0.3539 (OUTLIER) cc_final: 0.1315 (t80) REVERT: 3 118 GLU cc_start: 0.6064 (pt0) cc_final: 0.5381 (pt0) REVERT: 4 51 ARG cc_start: 0.8319 (mmt-90) cc_final: 0.8078 (mmp80) REVERT: 5 51 ARG cc_start: 0.7510 (mmp80) cc_final: 0.7248 (mmt180) REVERT: 6 25 MET cc_start: 0.7710 (ttm) cc_final: 0.7441 (ttp) REVERT: 7 44 LYS cc_start: 0.8381 (tppt) cc_final: 0.7957 (tptp) REVERT: 7 51 ARG cc_start: 0.8364 (mmt-90) cc_final: 0.7429 (mmt180) REVERT: 7 205 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.5314 (mp0) outliers start: 86 outliers final: 80 residues processed: 473 average time/residue: 0.3456 time to fit residues: 254.0901 Evaluate side-chains 487 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 402 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 217 ASP Chi-restraints excluded: chain 1 residue 14 THR Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 163 GLU Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 75 ASN Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 14 THR Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 187 ASP Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 136 ASP Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 189 optimal weight: 0.9980 chunk 254 optimal weight: 3.9990 chunk 73 optimal weight: 0.0870 chunk 220 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 239 optimal weight: 0.0970 chunk 100 optimal weight: 0.0980 chunk 245 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.185161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.144798 restraints weight = 25880.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.149168 restraints weight = 16613.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.152506 restraints weight = 12578.765| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.908 24143 Z= 0.942 Angle : 0.638 29.254 32571 Z= 0.341 Chirality : 0.046 0.270 3773 Planarity : 0.004 0.090 4193 Dihedral : 5.278 87.611 3400 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 3.59 % Allowed : 22.49 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.04 (0.15), residues: 3031 helix: 1.28 (0.15), residues: 1262 sheet: -0.09 (0.19), residues: 630 loop : -1.47 (0.17), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 73 PHE 0.026 0.001 PHE 5 211 TYR 0.014 0.001 TYR E 213 ARG 0.022 0.001 ARG 5 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5660.10 seconds wall clock time: 102 minutes 18.06 seconds (6138.06 seconds total)