Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 01:21:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylx_10841/04_2023/6ylx_10841.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylx_10841/04_2023/6ylx_10841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylx_10841/04_2023/6ylx_10841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylx_10841/04_2023/6ylx_10841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylx_10841/04_2023/6ylx_10841.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylx_10841/04_2023/6ylx_10841.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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: 5 Type Number sf(0) Gaussians P 2757 5.49 5 S 141 5.16 5 C 64385 2.51 5 N 21739 2.21 5 O 29860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B ASP 61": "OD1" <-> "OD2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 140": "OD1" <-> "OD2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B ASP 320": "OD1" <-> "OD2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 259": "OD1" <-> "OD2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "E TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 142": "OD1" <-> "OD2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 54": "OE1" <-> "OE2" Residue "G TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 227": "OD1" <-> "OD2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H ASP 107": "OD1" <-> "OD2" Residue "H PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 166": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "H ASP 171": "OD1" <-> "OD2" Residue "H ARG 173": "NH1" <-> "NH2" Residue "H PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 190": "OD1" <-> "OD2" Residue "K ARG 34": "NH1" <-> "NH2" Residue "K GLU 35": "OE1" <-> "OE2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 120": "OD1" <-> "OD2" Residue "K ASP 131": "OD1" <-> "OD2" Residue "K ASP 142": "OD1" <-> "OD2" Residue "K TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 170": "NH1" <-> "NH2" Residue "K ASP 184": "OD1" <-> "OD2" Residue "K GLU 203": "OE1" <-> "OE2" Residue "K GLU 216": "OE1" <-> "OE2" Residue "K TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 240": "NH1" <-> "NH2" Residue "K PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 261": "OD1" <-> "OD2" Residue "K ARG 277": "NH1" <-> "NH2" Residue "K PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 285": "NH1" <-> "NH2" Residue "K TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 299": "OD1" <-> "OD2" Residue "K GLU 302": "OE1" <-> "OE2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 73": "NH1" <-> "NH2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 171": "NH1" <-> "NH2" Residue "L PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 189": "OE1" <-> "OE2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "N TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 17": "OD1" <-> "OD2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N GLU 29": "OE1" <-> "OE2" Residue "N PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 124": "OD1" <-> "OD2" Residue "N ASP 136": "OD1" <-> "OD2" Residue "N GLU 160": "OE1" <-> "OE2" Residue "N PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 56": "OD1" <-> "OD2" Residue "O PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 31": "OE1" <-> "OE2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P ASP 108": "OD1" <-> "OD2" Residue "P ARG 126": "NH1" <-> "NH2" Residue "P TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P ARG 181": "NH1" <-> "NH2" Residue "Q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "Q PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 5": "NH1" <-> "NH2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R ARG 62": "NH1" <-> "NH2" Residue "R ARG 104": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "R ASP 111": "OD1" <-> "OD2" Residue "R TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 148": "OD1" <-> "OD2" Residue "R GLU 152": "OE1" <-> "OE2" Residue "S PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 96": "OD1" <-> "OD2" Residue "S TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S GLU 130": "OE1" <-> "OE2" Residue "S ASP 134": "OD1" <-> "OD2" Residue "S PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 147": "OD1" <-> "OD2" Residue "S TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "T ARG 108": "NH1" <-> "NH2" Residue "T GLU 137": "OE1" <-> "OE2" Residue "T ARG 139": "NH1" <-> "NH2" Residue "T TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 39": "OD1" <-> "OD2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 102": "OE1" <-> "OE2" Residue "U TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 113": "OE1" <-> "OE2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V ARG 88": "NH1" <-> "NH2" Residue "V ASP 89": "OD1" <-> "OD2" Residue "V PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 124": "OD1" <-> "OD2" Residue "W ARG 31": "NH1" <-> "NH2" Residue "W ASP 35": "OD1" <-> "OD2" Residue "W TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W GLU 79": "OE1" <-> "OE2" Residue "W ARG 81": "NH1" <-> "NH2" Residue "W TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 106": "OD1" <-> "OD2" Residue "W GLU 107": "OE1" <-> "OE2" Residue "W TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 152": "OE1" <-> "OE2" Residue "W GLU 162": "OE1" <-> "OE2" Residue "W ARG 166": "NH1" <-> "NH2" Residue "W PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 196": "OD1" <-> "OD2" Residue "W ARG 198": "NH1" <-> "NH2" Residue "X TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 125": "NH1" <-> "NH2" Residue "X ASP 129": "OD1" <-> "OD2" Residue "X TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 131": "OD1" <-> "OD2" Residue "X ASP 134": "OD1" <-> "OD2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "X TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y ASP 53": "OD1" <-> "OD2" Residue "Y ASP 54": "OD1" <-> "OD2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Y GLU 127": "OE1" <-> "OE2" Residue "Z GLU 31": "OE1" <-> "OE2" Residue "Z GLU 47": "OE1" <-> "OE2" Residue "Z PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 84": "NH1" <-> "NH2" Residue "Z ASP 88": "OD1" <-> "OD2" Residue "Z PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 102": "OE1" <-> "OE2" Residue "Z GLU 108": "OE1" <-> "OE2" Residue "Z ARG 135": "NH1" <-> "NH2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "a ASP 76": "OD1" <-> "OD2" Residue "a ASP 85": "OD1" <-> "OD2" Residue "a PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 136": "OE1" <-> "OE2" Residue "b ASP 19": "OD1" <-> "OD2" Residue "b ARG 24": "NH1" <-> "NH2" Residue "b ARG 27": "NH1" <-> "NH2" Residue "b ARG 34": "NH1" <-> "NH2" Residue "b ARG 43": "NH1" <-> "NH2" Residue "b TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 55": "OE1" <-> "OE2" Residue "b GLU 62": "OE1" <-> "OE2" Residue "b ASP 63": "OD1" <-> "OD2" Residue "b ASP 73": "OD1" <-> "OD2" Residue "b ARG 79": "NH1" <-> "NH2" Residue "b ASP 83": "OD1" <-> "OD2" Residue "b GLU 87": "OE1" <-> "OE2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ASP 111": "OD1" <-> "OD2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 135": "NH1" <-> "NH2" Residue "b ARG 154": "NH1" <-> "NH2" Residue "b ASP 191": "OD1" <-> "OD2" Residue "b ASP 193": "OD1" <-> "OD2" Residue "b TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 226": "OD1" <-> "OD2" Residue "b PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 255": "OD1" <-> "OD2" Residue "b GLU 258": "OE1" <-> "OE2" Residue "b PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 291": "OD1" <-> "OD2" Residue "b GLU 296": "OE1" <-> "OE2" Residue "b ARG 302": "NH1" <-> "NH2" Residue "b GLU 311": "OE1" <-> "OE2" Residue "b GLU 326": "OE1" <-> "OE2" Residue "b ARG 332": "NH1" <-> "NH2" Residue "b GLU 345": "OE1" <-> "OE2" Residue "b ASP 370": "OD1" <-> "OD2" Residue "b PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 380": "OE1" <-> "OE2" Residue "b ASP 389": "OD1" <-> "OD2" Residue "b PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 423": "OE1" <-> "OE2" Residue "b TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 459": "OE1" <-> "OE2" Residue "b PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 47": "OD1" <-> "OD2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "d TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 70": "NH1" <-> "NH2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "d GLU 111": "OE1" <-> "OE2" Residue "e PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 95": "OE1" <-> "OE2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "f PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 30": "OE1" <-> "OE2" Residue "h GLU 60": "OE1" <-> "OE2" Residue "h TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 79": "OD1" <-> "OD2" Residue "h ARG 105": "NH1" <-> "NH2" Residue "h TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "k GLU 13": "OE1" <-> "OE2" Residue "k PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 2": "NH1" <-> "NH2" Residue "n ARG 13": "NH1" <-> "NH2" Residue "n PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 18": "NH1" <-> "NH2" Residue "n ARG 34": "NH1" <-> "NH2" Residue "n GLU 45": "OE1" <-> "OE2" Residue "n PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 67": "OD1" <-> "OD2" Residue "n ARG 88": "NH1" <-> "NH2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n GLU 98": "OE1" <-> "OE2" Residue "n ARG 104": "NH1" <-> "NH2" Residue "n GLU 107": "OE1" <-> "OE2" Residue "n ARG 109": "NH1" <-> "NH2" Residue "n TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 120": "OE1" <-> "OE2" Residue "n ASP 134": "OD1" <-> "OD2" Residue "n PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 174": "NH1" <-> "NH2" Residue "n TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 196": "OE1" <-> "OE2" Residue "n PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 207": "OE1" <-> "OE2" Residue "n PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 239": "OD1" <-> "OD2" Residue "n GLU 265": "OE1" <-> "OE2" Residue "n PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 369": "NH1" <-> "NH2" Residue "n ASP 374": "OD1" <-> "OD2" Residue "n ARG 414": "NH1" <-> "NH2" Residue "n TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 434": "OD1" <-> "OD2" Residue "n GLU 440": "OE1" <-> "OE2" Residue "n TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 116": "OD1" <-> "OD2" Residue "o ARG 121": "NH1" <-> "NH2" Residue "o TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 198": "OD1" <-> "OD2" Residue "o GLU 205": "OE1" <-> "OE2" Residue "o ARG 207": "NH1" <-> "NH2" Residue "o PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 245": "OE1" <-> "OE2" Residue "q ARG 248": "NH1" <-> "NH2" Residue "q GLU 249": "OE1" <-> "OE2" Residue "q GLU 251": "OE1" <-> "OE2" Residue "q ARG 252": "NH1" <-> "NH2" Residue "q ARG 263": "NH1" <-> "NH2" Residue "q ASP 404": "OD1" <-> "OD2" Residue "q TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 418": "OD1" <-> "OD2" Residue "q ARG 421": "NH1" <-> "NH2" Residue "r TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 8": "OE1" <-> "OE2" Residue "r ARG 9": "NH1" <-> "NH2" Residue "r ASP 19": "OD1" <-> "OD2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 130": "OE1" <-> "OE2" Residue "r ARG 149": "NH1" <-> "NH2" Residue "r PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 188": "OE1" <-> "OE2" Residue "r GLU 248": "OE1" <-> "OE2" Residue "r ASP 250": "OD1" <-> "OD2" Residue "r ARG 251": "NH1" <-> "NH2" Residue "s ARG 2": "NH1" <-> "NH2" Residue "s ARG 6": "NH1" <-> "NH2" Residue "t GLU 17": "OE1" <-> "OE2" Residue "t ASP 27": "OD1" <-> "OD2" Residue "t GLU 43": "OE1" <-> "OE2" Residue "t ARG 74": "NH1" <-> "NH2" Residue "t ARG 77": "NH1" <-> "NH2" Residue "t GLU 82": "OE1" <-> "OE2" Residue "t GLU 89": "OE1" <-> "OE2" Residue "t ASP 98": "OD1" <-> "OD2" Residue "t ARG 130": "NH1" <-> "NH2" Residue "t ARG 146": "NH1" <-> "NH2" Residue "t ARG 148": "NH1" <-> "NH2" Residue "t PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 205": "NH1" <-> "NH2" Residue "t ARG 211": "NH1" <-> "NH2" Residue "t ARG 213": "NH1" <-> "NH2" Residue "t GLU 223": "OE1" <-> "OE2" Residue "t GLU 226": "OE1" <-> "OE2" Residue "t GLU 248": "OE1" <-> "OE2" Residue "t ASP 249": "OD1" <-> "OD2" Residue "t GLU 259": "OE1" <-> "OE2" Residue "t PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 293": "OE1" <-> "OE2" Residue "t GLU 295": "OE1" <-> "OE2" Residue "t ARG 299": "NH1" <-> "NH2" Residue "t PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 311": "OE1" <-> "OE2" Residue "t ASP 313": "OD1" <-> "OD2" Residue "u ARG 2": "NH1" <-> "NH2" Residue "u TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 23": "NH1" <-> "NH2" Residue "u ASP 25": "OD1" <-> "OD2" Residue "u PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 43": "NH1" <-> "NH2" Residue "u ARG 44": "NH1" <-> "NH2" Residue "u ARG 56": "NH1" <-> "NH2" Residue "u ASP 66": "OD1" <-> "OD2" Residue "u PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 75": "NH1" <-> "NH2" Residue "u ARG 80": "NH1" <-> "NH2" Residue "u ARG 83": "NH1" <-> "NH2" Residue "u GLU 84": "OE1" <-> "OE2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "u ARG 111": "NH1" <-> "NH2" Residue "u ARG 113": "NH1" <-> "NH2" Residue "u ASP 119": "OD1" <-> "OD2" Residue "u PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 122": "NH1" <-> "NH2" Residue "y PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 12": "OE1" <-> "OE2" Residue "y PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 39": "OE1" <-> "OE2" Residue "y ASP 44": "OD1" <-> "OD2" Residue "y GLU 80": "OE1" <-> "OE2" Residue "y ARG 85": "NH1" <-> "NH2" Residue "y ASP 90": "OD1" <-> "OD2" Residue "y ARG 100": "NH1" <-> "NH2" Residue "y ASP 120": "OD1" <-> "OD2" Residue "y ASP 122": "OD1" <-> "OD2" Residue "y GLU 127": "OE1" <-> "OE2" Residue "y ASP 131": "OD1" <-> "OD2" Residue "y ASP 169": "OD1" <-> "OD2" Residue "y ASP 209": "OD1" <-> "OD2" Residue "y ASP 226": "OD1" <-> "OD2" Residue "y ASP 238": "OD1" <-> "OD2" Residue "y GLU 242": "OE1" <-> "OE2" Residue "y TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 6": "NH1" <-> "NH2" Residue "z PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z GLU 30": "OE1" <-> "OE2" Residue "z ASP 35": "OD1" <-> "OD2" Residue "w PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 52": "OD1" <-> "OD2" Residue "w ASP 78": "OD1" <-> "OD2" Residue "w GLU 98": "OE1" <-> "OE2" Residue "w ASP 119": "OD1" <-> "OD2" Residue "w PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 148": "OE1" <-> "OE2" Residue "w ASP 165": "OD1" <-> "OD2" Residue "w GLU 181": "OE1" <-> "OE2" Residue "w ASP 214": "OD1" <-> "OD2" Residue "w ASP 224": "OD1" <-> "OD2" Residue "w ASP 261": "OD1" <-> "OD2" Residue "w PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 305": "OE1" <-> "OE2" Residue "w ARG 690": "NH1" <-> "NH2" Residue "w GLU 705": "OE1" <-> "OE2" Residue "w GLU 716": "OE1" <-> "OE2" Residue "w GLU 826": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 118882 Number of models: 1 Model: "" Number of chains: 47 Chain: "B" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3081 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Chain: "C" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2749 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain: "E" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1239 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "F" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "G" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1515 Classifications: {'peptide': 192} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 181} Chain: "H" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 184} Chain: "K" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 244} Chain breaks: 1 Chain: "L" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1499 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "M" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1059 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "N" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1543 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain breaks: 1 Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1397 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain breaks: 1 Chain: "Q" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1035 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "R" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1258 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "S" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1437 Classifications: {'peptide': 171} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "T" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 50} Chain: "U" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 844 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "V" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "W" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1885 Classifications: {'peptide': 234} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 222} Chain: "X" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1100 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "Y" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "a" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 735 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain: "b" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3814 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 445} Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "d" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 873 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "e" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "g" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 771 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "j" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 681 Classifications: {'peptide': 87} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 84} Chain: "k" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "l" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "n" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3030 Classifications: {'peptide': 371} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 346} Chain breaks: 2 Chain: "o" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1107 Classifications: {'peptide': 133} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 127} Chain: "q" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 723 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain breaks: 1 Chain: "r" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1760 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 8, 'TRANS': 208} Chain breaks: 2 Chain: "s" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 301 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "t" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2306 Classifications: {'peptide': 287} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Chain: "u" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1040 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "y" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1849 Classifications: {'peptide': 244} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 234} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 444 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "1" Number of atoms: 54232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2534, 54232 Classifications: {'RNA': 2534} Modifications used: {'rna2p_pur': 274, 'rna2p_pyr': 188, 'rna3p_pur': 1140, 'rna3p_pyr': 932} Link IDs: {'rna2p': 462, 'rna3p': 2071} Chain breaks: 10 Chain: "2" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 17, 'rna3p_pur': 63, 'rna3p_pyr': 63} Link IDs: {'rna2p': 31, 'rna3p': 126} Chain: "6" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1370 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 17, 'rna3p_pur': 21, 'rna3p_pyr': 19} Link IDs: {'rna2p': 24, 'rna3p': 40} Chain breaks: 1 Chain: "w" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2898 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 15, 'TRANS': 344} Chain breaks: 4 Residues with excluded nonbonded symmetry interactions: 199 residue: pdb=" N VAL O 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 13 " occ=0.50 residue: pdb=" N HIS O 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2 HIS O 14 " occ=0.50 ... (remaining 187 not shown) Time building chain proxies: 42.94, per 1000 atoms: 0.36 Number of scatterers: 118882 At special positions: 0 Unit cell: (215.716, 196.204, 321.948, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 141 16.00 P 2757 15.00 O 29860 8.00 N 21739 7.00 C 64385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 47 " distance=2.08 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 81 " distance=2.04 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 81 " distance=2.06 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 84 " distance=2.00 Simple disulfide: pdb=" SG CYS u 6 " - pdb=" SG CYS u 9 " distance=2.06 Simple disulfide: pdb=" SG CYS u 9 " - pdb=" SG CYS u 32 " distance=2.02 Simple disulfide: pdb=" SG CYS u 9 " - pdb=" SG CYS u 36 " distance=1.96 Simple disulfide: pdb=" SG CYS u 32 " - pdb=" SG CYS u 36 " distance=2.08 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: 45.69 Conformation dependent library (CDL) restraints added in 7.2 seconds 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14156 Finding SS restraints... Secondary structure from input PDB file: 266 helices and 74 sheets defined 42.4% alpha, 12.7% beta 790 base pairs and 1268 stacking pairs defined. Time for finding SS restraints: 29.73 Creating SS restraints... Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 142 through 154 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.539A pdb=" N GLY B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.661A pdb=" N LEU B 351 " --> pdb=" O ARG B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'C' and resid 31 through 44 removed outlier: 4.215A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 129 Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 153 through 159 removed outlier: 3.793A pdb=" N ILE C 159 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 181 Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.681A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 292 through 299 Processing helix chain 'C' and resid 320 through 327 Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 97 through 101 removed outlier: 4.035A pdb=" N LYS E 100 " --> pdb=" O ASN E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 131 through 150 removed outlier: 4.022A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'F' and resid 27 through 72 Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 120 through 130 removed outlier: 3.903A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 166 through 174 Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 222 through 226 Processing helix chain 'F' and resid 235 through 244 Processing helix chain 'G' and resid 53 through 69 Processing helix chain 'G' and resid 83 through 95 removed outlier: 3.778A pdb=" N ALA G 87 " --> pdb=" O ASP G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 118 removed outlier: 4.253A pdb=" N ALA G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU G 118 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 173 Processing helix chain 'G' and resid 183 through 190 Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 207 through 223 Processing helix chain 'G' and resid 226 through 230 removed outlier: 3.752A pdb=" N VAL G 229 " --> pdb=" O TYR G 226 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS G 230 " --> pdb=" O ASP G 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 226 through 230' Processing helix chain 'H' and resid 61 through 84 Processing helix chain 'H' and resid 116 through 120 Processing helix chain 'H' and resid 150 through 165 removed outlier: 3.875A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 50 removed outlier: 3.795A pdb=" N LYS K 50 " --> pdb=" O LYS K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 77 Processing helix chain 'K' and resid 106 through 115 Processing helix chain 'K' and resid 130 through 134 removed outlier: 3.914A pdb=" N LYS K 133 " --> pdb=" O SER K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 148 removed outlier: 4.241A pdb=" N LEU K 140 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP K 145 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER K 146 " --> pdb=" O ASP K 142 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU K 147 " --> pdb=" O GLN K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 163 Processing helix chain 'K' and resid 166 through 176 removed outlier: 4.303A pdb=" N GLN K 176 " --> pdb=" O ALA K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 193 removed outlier: 3.968A pdb=" N THR K 188 " --> pdb=" O SER K 185 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU K 190 " --> pdb=" O VAL K 187 " (cutoff:3.500A) Proline residue: K 191 - end of helix Processing helix chain 'K' and resid 195 through 201 removed outlier: 3.857A pdb=" N TYR K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS K 201 " --> pdb=" O LYS K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 219 through 224 Processing helix chain 'K' and resid 224 through 232 Processing helix chain 'K' and resid 255 through 271 removed outlier: 3.658A pdb=" N ASP K 261 " --> pdb=" O GLU K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 299 No H-bonds generated for 'chain 'K' and resid 297 through 299' Processing helix chain 'K' and resid 300 through 305 removed outlier: 3.806A pdb=" N LYS K 305 " --> pdb=" O LEU K 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 94 removed outlier: 4.316A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'L' and resid 140 through 145 Processing helix chain 'L' and resid 166 through 193 removed outlier: 5.174A pdb=" N GLY L 181 " --> pdb=" O LYS L 177 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE L 182 " --> pdb=" O LYS L 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 97 removed outlier: 3.913A pdb=" N LYS M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 111 Processing helix chain 'M' and resid 113 through 135 Processing helix chain 'N' and resid 3 through 12 Processing helix chain 'N' and resid 16 through 33 Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 153 through 157 removed outlier: 3.824A pdb=" N HIS N 156 " --> pdb=" O ASP N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 186 through 195 Processing helix chain 'O' and resid 15 through 29 Processing helix chain 'O' and resid 46 through 60 Processing helix chain 'O' and resid 75 through 88 Processing helix chain 'O' and resid 92 through 100 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 145 Processing helix chain 'O' and resid 149 through 186 removed outlier: 3.555A pdb=" N VAL O 153 " --> pdb=" O TYR O 149 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS O 155 " --> pdb=" O ASP O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 197 Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 25 through 37 removed outlier: 4.944A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 52 removed outlier: 3.891A pdb=" N LEU P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 71 through 76 removed outlier: 4.102A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'P' and resid 169 through 183 Processing helix chain 'Q' and resid 23 through 40 Processing helix chain 'Q' and resid 42 through 53 removed outlier: 4.538A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 72 Processing helix chain 'Q' and resid 107 through 118 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 22 Processing helix chain 'R' and resid 28 through 35 Processing helix chain 'R' and resid 37 through 47 Processing helix chain 'R' and resid 60 through 72 Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 112 Processing helix chain 'R' and resid 116 through 129 Processing helix chain 'R' and resid 134 through 157 Processing helix chain 'S' and resid 33 through 49 Processing helix chain 'S' and resid 98 through 115 Processing helix chain 'S' and resid 140 through 145 removed outlier: 4.222A pdb=" N THR S 145 " --> pdb=" O GLN S 142 " (cutoff:3.500A) Processing helix chain 'T' and resid 102 through 122 Processing helix chain 'U' and resid 19 through 25 Processing helix chain 'U' and resid 29 through 41 removed outlier: 4.034A pdb=" N TYR U 33 " --> pdb=" O ASP U 29 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP U 39 " --> pdb=" O LYS U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 87 Processing helix chain 'V' and resid 119 through 126 Processing helix chain 'V' and resid 126 through 132 removed outlier: 3.909A pdb=" N ALA V 130 " --> pdb=" O TRP V 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 37 removed outlier: 3.870A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR W 36 " --> pdb=" O GLU W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 60 Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 89 through 96 removed outlier: 3.753A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS W 96 " --> pdb=" O LEU W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 119 removed outlier: 4.150A pdb=" N VAL W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 161 through 168 Processing helix chain 'W' and resid 196 through 207 Processing helix chain 'X' and resid 4 through 17 Processing helix chain 'X' and resid 58 through 63 Processing helix chain 'X' and resid 69 through 79 removed outlier: 3.645A pdb=" N GLU X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 104 Processing helix chain 'X' and resid 132 through 140 Processing helix chain 'Y' and resid 11 through 21 Processing helix chain 'Y' and resid 23 through 31 removed outlier: 4.372A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 75 through 78 Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 122 Processing helix chain 'Z' and resid 59 through 66 Processing helix chain 'Z' and resid 105 through 123 removed outlier: 3.832A pdb=" N GLU Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL Z 113 " --> pdb=" O GLU Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 132 Processing helix chain 'a' and resid 83 through 92 removed outlier: 4.185A pdb=" N GLN a 89 " --> pdb=" O ASP a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 108 Processing helix chain 'a' and resid 131 through 141 Processing helix chain 'b' and resid 13 through 29 Processing helix chain 'b' and resid 38 through 66 Processing helix chain 'b' and resid 75 through 86 Processing helix chain 'b' and resid 87 through 117 Processing helix chain 'b' and resid 121 through 142 Processing helix chain 'b' and resid 143 through 159 removed outlier: 4.067A pdb=" N LEU b 147 " --> pdb=" O LEU b 143 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA b 148 " --> pdb=" O ARG b 144 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 188 Processing helix chain 'b' and resid 233 through 246 Processing helix chain 'b' and resid 263 through 274 Processing helix chain 'b' and resid 294 through 298 removed outlier: 3.576A pdb=" N ASP b 297 " --> pdb=" O ARG b 294 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 311 Processing helix chain 'b' and resid 325 through 348 Processing helix chain 'b' and resid 353 through 362 removed outlier: 4.439A pdb=" N LEU b 358 " --> pdb=" O ILE b 354 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ASN b 359 " --> pdb=" O ASN b 355 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS b 360 " --> pdb=" O ASN b 356 " (cutoff:3.500A) Processing helix chain 'b' and resid 380 through 385 Processing helix chain 'b' and resid 399 through 407 removed outlier: 4.429A pdb=" N GLY b 407 " --> pdb=" O GLU b 403 " (cutoff:3.500A) Processing helix chain 'b' and resid 425 through 429 removed outlier: 3.835A pdb=" N ASN b 429 " --> pdb=" O GLU b 426 " (cutoff:3.500A) Processing helix chain 'b' and resid 440 through 444 removed outlier: 3.711A pdb=" N ASP b 443 " --> pdb=" O ASN b 440 " (cutoff:3.500A) Processing helix chain 'b' and resid 448 through 467 removed outlier: 3.832A pdb=" N GLU b 466 " --> pdb=" O LYS b 462 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 20 removed outlier: 3.709A pdb=" N LYS c 19 " --> pdb=" O ALA c 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 49 through 64 Processing helix chain 'c' and resid 73 through 82 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 24 through 26 No H-bonds generated for 'chain 'd' and resid 24 through 26' Processing helix chain 'd' and resid 27 through 44 Processing helix chain 'd' and resid 52 through 61 Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'e' and resid 101 through 116 removed outlier: 4.213A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 42 Processing helix chain 'g' and resid 58 through 62 Processing helix chain 'g' and resid 67 through 71 Processing helix chain 'g' and resid 82 through 113 Processing helix chain 'h' and resid 5 through 10 Processing helix chain 'h' and resid 13 through 35 Processing helix chain 'h' and resid 42 through 70 removed outlier: 3.783A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 90 Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 77 removed outlier: 7.600A pdb=" N GLU i 66 " --> pdb=" O ARG i 62 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N LYS i 67 " --> pdb=" O ASN i 63 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG i 68 " --> pdb=" O SER i 64 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 100 Processing helix chain 'j' and resid 4 through 10 Processing helix chain 'j' and resid 50 through 58 removed outlier: 4.021A pdb=" N HIS j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 69 through 76 Processing helix chain 'k' and resid 7 through 16 Processing helix chain 'k' and resid 58 through 69 Processing helix chain 'l' and resid 6 through 20 Processing helix chain 'l' and resid 24 through 28 Processing helix chain 'n' and resid 5 through 9 removed outlier: 3.578A pdb=" N THR n 8 " --> pdb=" O LYS n 5 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG n 9 " --> pdb=" O LYS n 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 5 through 9' Processing helix chain 'n' and resid 10 through 15 Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 40 removed outlier: 4.443A pdb=" N GLY n 40 " --> pdb=" O CYS n 36 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 53 Processing helix chain 'n' and resid 64 through 74 removed outlier: 4.358A pdb=" N HIS n 73 " --> pdb=" O GLN n 69 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU n 74 " --> pdb=" O TYR n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 74 through 97 removed outlier: 4.184A pdb=" N ALA n 78 " --> pdb=" O GLU n 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS n 79 " --> pdb=" O PRO n 75 " (cutoff:3.500A) Processing helix chain 'n' and resid 98 through 108 Processing helix chain 'n' and resid 114 through 122 Processing helix chain 'n' and resid 124 through 131 Processing helix chain 'n' and resid 132 through 145 removed outlier: 3.527A pdb=" N MET n 138 " --> pdb=" O ASP n 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN n 144 " --> pdb=" O PHE n 140 " (cutoff:3.500A) Processing helix chain 'n' and resid 153 through 174 Processing helix chain 'n' and resid 215 through 241 Processing helix chain 'n' and resid 249 through 256 removed outlier: 3.801A pdb=" N ILE n 255 " --> pdb=" O LYS n 251 " (cutoff:3.500A) Processing helix chain 'n' and resid 376 through 383 Processing helix chain 'n' and resid 391 through 394 removed outlier: 3.516A pdb=" N ASP n 394 " --> pdb=" O ALA n 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 391 through 394' Processing helix chain 'n' and resid 429 through 439 Processing helix chain 'o' and resid 103 through 112 Processing helix chain 'o' and resid 141 through 153 Processing helix chain 'o' and resid 192 through 215 removed outlier: 4.616A pdb=" N GLY o 215 " --> pdb=" O LEU o 211 " (cutoff:3.500A) Processing helix chain 'q' and resid 230 through 266 removed outlier: 3.680A pdb=" N TRP q 234 " --> pdb=" O ASN q 230 " (cutoff:3.500A) Processing helix chain 'q' and resid 405 through 409 Processing helix chain 'q' and resid 414 through 427 Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 20 through 41 removed outlier: 4.510A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER r 36 " --> pdb=" O SER r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 45 through 73 Processing helix chain 'r' and resid 187 through 190 removed outlier: 3.651A pdb=" N GLY r 190 " --> pdb=" O PRO r 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 187 through 190' Processing helix chain 'r' and resid 207 through 213 removed outlier: 3.855A pdb=" N GLN r 211 " --> pdb=" O PRO r 207 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 35 removed outlier: 4.148A pdb=" N LYS s 35 " --> pdb=" O LYS s 31 " (cutoff:3.500A) Processing helix chain 't' and resid 16 through 53 removed outlier: 4.305A pdb=" N LEU t 20 " --> pdb=" O PRO t 16 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER t 50 " --> pdb=" O LYS t 46 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS t 52 " --> pdb=" O LYS t 48 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN t 53 " --> pdb=" O ARG t 49 " (cutoff:3.500A) Processing helix chain 't' and resid 57 through 88 Processing helix chain 't' and resid 156 through 167 removed outlier: 5.292A pdb=" N ILE t 162 " --> pdb=" O LYS t 158 " (cutoff:3.500A) Processing helix chain 't' and resid 183 through 191 removed outlier: 3.598A pdb=" N LYS t 188 " --> pdb=" O TYR t 184 " (cutoff:3.500A) Processing helix chain 't' and resid 200 through 211 Processing helix chain 't' and resid 231 through 240 removed outlier: 3.561A pdb=" N VAL t 235 " --> pdb=" O ASP t 231 " (cutoff:3.500A) Processing helix chain 't' and resid 241 through 243 No H-bonds generated for 'chain 't' and resid 241 through 243' Processing helix chain 't' and resid 247 through 256 Processing helix chain 't' and resid 261 through 268 Processing helix chain 't' and resid 281 through 299 removed outlier: 3.666A pdb=" N ARG t 287 " --> pdb=" O LEU t 283 " (cutoff:3.500A) Processing helix chain 't' and resid 313 through 322 removed outlier: 3.680A pdb=" N ALA t 319 " --> pdb=" O ASP t 315 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS t 320 " --> pdb=" O SER t 316 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 52 through 59 removed outlier: 4.032A pdb=" N ALA u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) Processing helix chain 'u' and resid 66 through 72 removed outlier: 3.850A pdb=" N PHE u 71 " --> pdb=" O THR u 68 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA u 72 " --> pdb=" O LEU u 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 82 through 113 removed outlier: 4.060A pdb=" N LYS u 91 " --> pdb=" O ALA u 87 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU u 98 " --> pdb=" O ALA u 94 " (cutoff:3.500A) Processing helix chain 'u' and resid 114 through 123 removed outlier: 4.294A pdb=" N LYS u 118 " --> pdb=" O GLY u 114 " (cutoff:3.500A) Processing helix chain 'y' and resid 33 through 43 removed outlier: 3.920A pdb=" N GLU y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 44 through 46 No H-bonds generated for 'chain 'y' and resid 44 through 46' Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 134 removed outlier: 3.749A pdb=" N SER y 130 " --> pdb=" O GLU y 126 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 197 Processing helix chain 'y' and resid 211 through 223 Processing helix chain 'y' and resid 230 through 236 Processing helix chain 'y' and resid 237 through 244 removed outlier: 3.508A pdb=" N ILE y 241 " --> pdb=" O ARG y 237 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 20 Processing helix chain 'z' and resid 20 through 56 removed outlier: 4.046A pdb=" N LYS z 24 " --> pdb=" O GLY z 20 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA z 25 " --> pdb=" O VAL z 21 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL z 26 " --> pdb=" O PHE z 22 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN z 31 " --> pdb=" O ASP z 27 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU z 41 " --> pdb=" O LEU z 37 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU z 42 " --> pdb=" O LYS z 38 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS z 51 " --> pdb=" O GLU z 47 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU z 54 " --> pdb=" O LYS z 50 " (cutoff:3.500A) Processing helix chain 'w' and resid 27 through 31 removed outlier: 3.673A pdb=" N SER w 30 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE w 31 " --> pdb=" O ARG w 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 27 through 31' Processing helix chain 'w' and resid 32 through 40 removed outlier: 3.792A pdb=" N ILE w 36 " --> pdb=" O LYS w 32 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU w 38 " --> pdb=" O ILE w 34 " (cutoff:3.500A) Processing helix chain 'w' and resid 58 through 68 removed outlier: 3.740A pdb=" N VAL w 63 " --> pdb=" O SER w 59 " (cutoff:3.500A) Processing helix chain 'w' and resid 97 through 108 removed outlier: 3.837A pdb=" N ARG w 101 " --> pdb=" O THR w 97 " (cutoff:3.500A) Processing helix chain 'w' and resid 129 through 150 Processing helix chain 'w' and resid 165 through 177 Processing helix chain 'w' and resid 209 through 213 removed outlier: 3.738A pdb=" N LEU w 213 " --> pdb=" O PRO w 210 " (cutoff:3.500A) Processing helix chain 'w' and resid 259 through 265 Processing helix chain 'w' and resid 284 through 291 Processing helix chain 'w' and resid 299 through 304 Processing helix chain 'w' and resid 311 through 329 Processing helix chain 'w' and resid 696 through 705 removed outlier: 4.351A pdb=" N ASP w 702 " --> pdb=" O TRP w 698 " (cutoff:3.500A) Processing helix chain 'w' and resid 714 through 726 Processing helix chain 'w' and resid 820 through 838 removed outlier: 3.818A pdb=" N LYS w 824 " --> pdb=" O ASP w 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 355 through 359 removed outlier: 4.317A pdb=" N SER B 355 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE B 359 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE B 215 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS B 273 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS B 281 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE B 321 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP B 320 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR B 81 " --> pdb=" O ASP B 320 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 72 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL B 57 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU B 74 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N THR B 55 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 76 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N MET B 53 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 99 through 106 removed outlier: 6.305A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 88 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 162 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 179 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 225 through 227 removed outlier: 4.177A pdb=" N GLY B 225 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG B 270 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 268 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 6 through 8 removed outlier: 6.994A pdb=" N VAL C 6 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASN C 18 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 8 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.635A pdb=" N LEU C 150 " --> pdb=" O TRP C 250 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 79 removed outlier: 7.332A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 74 through 77 removed outlier: 3.689A pdb=" N VAL F 77 " --> pdb=" O ARG T 139 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG T 139 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.318A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AB2, first strand: chain 'G' and resid 177 through 180 removed outlier: 6.332A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 11 removed outlier: 6.882A pdb=" N ILE H 4 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL H 48 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=AB5, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.885A pdb=" N LYS H 87 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS H 184 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS H 89 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AB7, first strand: chain 'K' and resid 243 through 249 removed outlier: 5.364A pdb=" N ASN K 245 " --> pdb=" O VAL K 83 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL K 83 " --> pdb=" O ASN K 245 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N HIS K 247 " --> pdb=" O ILE K 81 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE K 81 " --> pdb=" O HIS K 247 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY K 249 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR K 292 " --> pdb=" O ILE K 279 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE K 281 " --> pdb=" O PRO K 290 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 97 through 101 Processing sheet with id=AB9, first strand: chain 'K' and resid 155 through 156 Processing sheet with id=AC1, first strand: chain 'L' and resid 22 through 25 Processing sheet with id=AC2, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AC3, first strand: chain 'L' and resid 123 through 126 removed outlier: 4.166A pdb=" N LYS h 115 " --> pdb=" O PHE L 126 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 156 through 157 removed outlier: 7.875A pdb=" N LYS a 126 " --> pdb=" O PRO a 100 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE a 102 " --> pdb=" O LYS a 126 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL a 125 " --> pdb=" O GLU a 146 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 14 through 16 Processing sheet with id=AC6, first strand: chain 'M' and resid 55 through 59 removed outlier: 5.484A pdb=" N ASP M 47 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ILE M 35 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 37 through 39 removed outlier: 3.767A pdb=" N ALA N 39 " --> pdb=" O ILE N 61 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR N 62 " --> pdb=" O VAL N 132 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TYR N 127 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLN N 123 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL N 135 " --> pdb=" O VAL N 115 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL N 115 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 6 through 10 removed outlier: 3.507A pdb=" N LYS O 103 " --> pdb=" O ILE O 33 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AD1, first strand: chain 'P' and resid 14 through 22 removed outlier: 5.883A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N THR P 151 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL P 114 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 58 through 59 removed outlier: 3.817A pdb=" N ILE P 58 " --> pdb=" O ARG P 82 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 128 through 130 removed outlier: 4.265A pdb=" N THR P 129 " --> pdb=" O ASN P 137 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN P 137 " --> pdb=" O THR P 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AD5, first strand: chain 'Q' and resid 120 through 122 removed outlier: 6.432A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL Q 81 " --> pdb=" O THR Q 100 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA Q 102 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR Q 80 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU Q 140 " --> pdb=" O THR Q 80 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL Q 82 " --> pdb=" O LEU Q 140 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 58 through 63 removed outlier: 6.850A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 88 through 96 removed outlier: 4.424A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 54 through 58 removed outlier: 8.566A pdb=" N TYR U 103 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR U 16 " --> pdb=" O TYR U 103 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU U 105 " --> pdb=" O THR U 16 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASP U 18 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N PHE U 107 " --> pdb=" O ASP U 18 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V' and resid 17 through 18 Processing sheet with id=AE1, first strand: chain 'V' and resid 22 through 24 removed outlier: 6.901A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL V 78 " --> pdb=" O VAL V 101 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL V 101 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 85 through 87 removed outlier: 4.214A pdb=" N VAL V 91 " --> pdb=" O ARG V 87 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 117 through 118 Processing sheet with id=AE4, first strand: chain 'W' and resid 64 through 66 removed outlier: 3.815A pdb=" N VAL W 42 " --> pdb=" O ALA W 219 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N HIS W 44 " --> pdb=" O VAL W 217 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL W 217 " --> pdb=" O HIS W 44 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS W 216 " --> pdb=" O ILE W 233 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE W 233 " --> pdb=" O LYS W 216 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 121 through 123 Processing sheet with id=AE6, first strand: chain 'W' and resid 136 through 137 Processing sheet with id=AE7, first strand: chain 'X' and resid 81 through 86 removed outlier: 3.739A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AE9, first strand: chain 'Y' and resid 79 through 82 removed outlier: 7.107A pdb=" N GLU Y 55 " --> pdb=" O THR Y 107 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 86 through 88 Processing sheet with id=AF2, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.386A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N HIS Z 40 " --> pdb=" O PRO Z 28 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE Z 46 " --> pdb=" O LYS Z 22 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS Z 22 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 72 through 73 Processing sheet with id=AF4, first strand: chain 'b' and resid 205 through 211 removed outlier: 3.849A pdb=" N CYS b 249 " --> pdb=" O THR b 169 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'b' and resid 363 through 364 removed outlier: 3.677A pdb=" N LEU y 181 " --> pdb=" O ALA b 364 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'c' and resid 21 through 25 removed outlier: 6.545A pdb=" N THR c 24 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE c 92 " --> pdb=" O THR c 24 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE c 42 " --> pdb=" O TYR c 68 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE c 70 " --> pdb=" O ILE c 42 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE c 44 " --> pdb=" O PHE c 70 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'd' and resid 49 through 50 removed outlier: 6.719A pdb=" N ARG d 50 " --> pdb=" O VAL d 93 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE d 90 " --> pdb=" O LYS d 78 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS d 78 " --> pdb=" O PHE d 90 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR d 9 " --> pdb=" O VAL d 109 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'e' and resid 72 through 76 removed outlier: 5.794A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'f' and resid 8 through 15 removed outlier: 6.907A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL f 80 " --> pdb=" O HIS f 75 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS f 75 " --> pdb=" O VAL f 80 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.493A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AG3, first strand: chain 'k' and resid 3 through 4 removed outlier: 6.557A pdb=" N ARG k 3 " --> pdb=" O THR k 53 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL k 55 " --> pdb=" O ARG k 3 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'n' and resid 178 through 181 Processing sheet with id=AG5, first strand: chain 'n' and resid 386 through 389 Processing sheet with id=AG6, first strand: chain 'o' and resid 119 through 124 removed outlier: 4.422A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU o 167 " --> pdb=" O SER o 90 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE o 92 " --> pdb=" O ARG o 165 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG o 165 " --> pdb=" O ILE o 92 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR o 94 " --> pdb=" O GLN o 163 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN o 163 " --> pdb=" O TYR o 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'r' and resid 149 through 150 removed outlier: 7.264A pdb=" N ARG r 149 " --> pdb=" O ILE r 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'r' and resid 181 through 185 removed outlier: 3.738A pdb=" N LYS r 201 " --> pdb=" O ILE r 220 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE r 220 " --> pdb=" O LYS r 201 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 't' and resid 129 through 133 Processing sheet with id=AH1, first strand: chain 't' and resid 194 through 195 removed outlier: 4.051A pdb=" N THR t 173 " --> pdb=" O ARG t 146 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 't' and resid 213 through 215 Processing sheet with id=AH3, first strand: chain 'u' and resid 4 through 5 Processing sheet with id=AH4, first strand: chain 'u' and resid 19 through 22 Processing sheet with id=AH5, first strand: chain 'y' and resid 2 through 4 removed outlier: 6.345A pdb=" N THR y 3 " --> pdb=" O THR y 206 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU y 203 " --> pdb=" O ASN y 200 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'y' and resid 17 through 19 Processing sheet with id=AH7, first strand: chain 'y' and resid 64 through 65 removed outlier: 3.822A pdb=" N ALA y 64 " --> pdb=" O LEU y 71 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'y' and resid 109 through 110 removed outlier: 3.770A pdb=" N CYS y 109 " --> pdb=" O LEU y 116 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'y' and resid 152 through 154 Processing sheet with id=AI1, first strand: chain 'w' and resid 88 through 92 removed outlier: 5.989A pdb=" N ILE w 74 " --> pdb=" O ILE w 89 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE w 91 " --> pdb=" O ILE w 74 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY w 76 " --> pdb=" O PHE w 91 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE w 51 " --> pdb=" O LEU w 117 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL w 116 " --> pdb=" O VAL w 157 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LYS w 159 " --> pdb=" O VAL w 116 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N HIS w 118 " --> pdb=" O LYS w 159 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N PHE w 161 " --> pdb=" O HIS w 118 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'w' and resid 795 through 797 2527 hydrogen bonds defined for protein. 7275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1971 hydrogen bonds 3294 hydrogen bond angles 0 basepair planarities 790 basepair parallelities 1268 stacking parallelities Total time for adding SS restraints: 130.37 Time building geometry restraints manager: 49.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 14979 1.30 - 1.45: 55888 1.45 - 1.60: 53558 1.60 - 1.74: 2294 1.74 - 1.89: 223 Bond restraints: 126942 Sorted by residual: bond pdb=" CA ALA N 146 " pdb=" C ALA N 146 " ideal model delta sigma weight residual 1.522 1.383 0.139 1.72e-02 3.38e+03 6.50e+01 bond pdb=" C LEU f 102 " pdb=" N TYR f 103 " ideal model delta sigma weight residual 1.327 1.159 0.168 2.31e-02 1.87e+03 5.32e+01 bond pdb=" C PRO B 96 " pdb=" N ARG B 97 " ideal model delta sigma weight residual 1.332 1.241 0.091 1.40e-02 5.10e+03 4.26e+01 bond pdb=" C ASP N 153 " pdb=" N PRO N 154 " ideal model delta sigma weight residual 1.337 1.265 0.072 1.11e-02 8.12e+03 4.16e+01 bond pdb=" CB PRO f 104 " pdb=" CG PRO f 104 " ideal model delta sigma weight residual 1.506 1.256 0.250 3.90e-02 6.57e+02 4.11e+01 ... (remaining 126937 not shown) Histogram of bond angle deviations from ideal: 91.98 - 102.01: 3815 102.01 - 112.04: 72399 112.04 - 122.06: 78884 122.06 - 132.09: 28922 132.09 - 142.11: 721 Bond angle restraints: 184741 Sorted by residual: angle pdb=" C ILE F 156 " pdb=" N ASN F 157 " pdb=" CA ASN F 157 " ideal model delta sigma weight residual 121.54 139.63 -18.09 1.91e+00 2.74e-01 8.97e+01 angle pdb=" N LYS n 5 " pdb=" CA LYS n 5 " pdb=" C LYS n 5 " ideal model delta sigma weight residual 110.91 119.41 -8.50 1.17e+00 7.31e-01 5.27e+01 angle pdb=" N VAL E 35 " pdb=" CA VAL E 35 " pdb=" C VAL E 35 " ideal model delta sigma weight residual 109.19 103.52 5.67 8.20e-01 1.49e+00 4.79e+01 angle pdb=" C ASN F 157 " pdb=" N LYS F 158 " pdb=" CA LYS F 158 " ideal model delta sigma weight residual 121.54 134.40 -12.86 1.91e+00 2.74e-01 4.53e+01 angle pdb=" C LYS r 16 " pdb=" CA LYS r 16 " pdb=" CB LYS r 16 " ideal model delta sigma weight residual 110.42 97.15 13.27 1.99e+00 2.53e-01 4.45e+01 ... (remaining 184736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 67693 36.00 - 72.00: 2841 72.00 - 108.00: 227 108.00 - 144.00: 37 144.00 - 180.00: 58 Dihedral angle restraints: 70856 sinusoidal: 49024 harmonic: 21832 Sorted by residual: dihedral pdb=" CA PRO n 123 " pdb=" C PRO n 123 " pdb=" N SER n 124 " pdb=" CA SER n 124 " ideal model delta harmonic sigma weight residual -180.00 -59.05 -120.95 0 5.00e+00 4.00e-02 5.85e+02 dihedral pdb=" CA ILE n 375 " pdb=" C ILE n 375 " pdb=" N LEU n 376 " pdb=" CA LEU n 376 " ideal model delta harmonic sigma weight residual 180.00 119.73 60.27 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA GLY n 55 " pdb=" C GLY n 55 " pdb=" N SER n 56 " pdb=" CA SER n 56 " ideal model delta harmonic sigma weight residual -180.00 -120.85 -59.15 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 70853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 19915 0.120 - 0.240: 2688 0.240 - 0.360: 276 0.360 - 0.480: 40 0.480 - 0.600: 9 Chirality restraints: 22928 Sorted by residual: chirality pdb=" CB VAL P 119 " pdb=" CA VAL P 119 " pdb=" CG1 VAL P 119 " pdb=" CG2 VAL P 119 " both_signs ideal model delta sigma weight residual False -2.63 -2.03 -0.60 2.00e-01 2.50e+01 8.99e+00 chirality pdb=" CB VAL O 145 " pdb=" CA VAL O 145 " pdb=" CG1 VAL O 145 " pdb=" CG2 VAL O 145 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.48e+00 chirality pdb=" CB VAL Y 8 " pdb=" CA VAL Y 8 " pdb=" CG1 VAL Y 8 " pdb=" CG2 VAL Y 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.56e+00 ... (remaining 22925 not shown) Planarity restraints: 13136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 2 15 " 0.083 2.00e-02 2.50e+03 3.63e-02 3.94e+01 pdb=" N9 G 2 15 " -0.081 2.00e-02 2.50e+03 pdb=" C8 G 2 15 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G 2 15 " -0.016 2.00e-02 2.50e+03 pdb=" C5 G 2 15 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G 2 15 " 0.030 2.00e-02 2.50e+03 pdb=" O6 G 2 15 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G 2 15 " 0.011 2.00e-02 2.50e+03 pdb=" C2 G 2 15 " 0.008 2.00e-02 2.50e+03 pdb=" N2 G 2 15 " -0.012 2.00e-02 2.50e+03 pdb=" N3 G 2 15 " -0.021 2.00e-02 2.50e+03 pdb=" C4 G 2 15 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA g 82 " -0.030 2.00e-02 2.50e+03 6.04e-02 3.65e+01 pdb=" C ALA g 82 " 0.105 2.00e-02 2.50e+03 pdb=" O ALA g 82 " -0.038 2.00e-02 2.50e+03 pdb=" N ASN g 83 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 166 " -0.030 2.00e-02 2.50e+03 5.95e-02 3.53e+01 pdb=" C ALA L 166 " 0.103 2.00e-02 2.50e+03 pdb=" O ALA L 166 " -0.038 2.00e-02 2.50e+03 pdb=" N PHE L 167 " -0.035 2.00e-02 2.50e+03 ... (remaining 13133 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 3489 2.61 - 3.18: 104730 3.18 - 3.75: 229630 3.75 - 4.33: 285447 4.33 - 4.90: 416905 Nonbonded interactions: 1040201 Sorted by model distance: nonbonded pdb=" O2' A 11303 " pdb=" O4' A 11304 " model vdw 2.033 2.440 nonbonded pdb=" OP1 C 1 339 " pdb=" O2' G 11380 " model vdw 2.042 2.440 nonbonded pdb=" O2' A 11433 " pdb=" O4' G 11434 " model vdw 2.048 2.440 nonbonded pdb=" O ASN e 99 " pdb=" O2' U 11388 " model vdw 2.053 2.440 nonbonded pdb=" O2' A 11524 " pdb=" OP2 U 11526 " model vdw 2.059 2.440 ... (remaining 1040196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 18.510 Check model and map are aligned: 1.260 Set scattering table: 0.740 Process input model: 332.020 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 361.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.019 0.286 126942 Z= 1.201 Angle : 1.572 18.094 184741 Z= 0.795 Chirality : 0.085 0.600 22928 Planarity : 0.010 0.120 13136 Dihedral : 17.825 179.997 56676 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.39 % Favored : 96.57 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.21 % Twisted Proline : 2.41 % Twisted General : 1.06 % 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: -3.91 (0.08), residues: 7377 helix: -2.20 (0.07), residues: 2863 sheet: -2.35 (0.15), residues: 916 loop : -2.99 (0.08), residues: 3598 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1871 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1829 time to evaluate : 6.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 26 residues processed: 1864 average time/residue: 1.1548 time to fit residues: 3542.9297 Evaluate side-chains 1380 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1354 time to evaluate : 6.522 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.8004 time to fit residues: 48.0032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 846 optimal weight: 0.9990 chunk 760 optimal weight: 0.9980 chunk 421 optimal weight: 20.0000 chunk 259 optimal weight: 2.9990 chunk 512 optimal weight: 0.9980 chunk 406 optimal weight: 9.9990 chunk 786 optimal weight: 4.9990 chunk 304 optimal weight: 20.0000 chunk 478 optimal weight: 0.9990 chunk 585 optimal weight: 8.9990 chunk 910 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN B 231 HIS C 58 HIS C 201 GLN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN F 146 GLN G 77 GLN G 192 GLN H 5 GLN H 50 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 GLN H 183 HIS K 42 ASN K 84 ASN K 262 ASN ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 ASN L 103 ASN L 112 ASN ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 182 ASN O 55 HIS O 182 ASN P 121 GLN S 138 GLN W 74 GLN Z 57 HIS ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 217 GLN b 288 ASN b 454 GLN c 75 ASN d 17 HIS d 43 HIS f 42 GLN f 77 ASN g 33 GLN h 59 ASN ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 437 ASN ** o 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 13 GLN ** r 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 44 GLN ** t 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 115 ASN ** y 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 82 GLN y 235 ASN z 31 GLN w 71 ASN w 92 GLN w 174 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.103 126942 Z= 0.206 Angle : 0.750 14.326 184741 Z= 0.378 Chirality : 0.040 0.342 22928 Planarity : 0.006 0.071 13136 Dihedral : 16.228 179.646 41320 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.12 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.34 % Twisted General : 0.24 % 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: -2.42 (0.09), residues: 7377 helix: -0.69 (0.09), residues: 2871 sheet: -1.65 (0.16), residues: 908 loop : -2.38 (0.09), residues: 3598 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1904 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1748 time to evaluate : 6.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 156 outliers final: 71 residues processed: 1822 average time/residue: 1.1033 time to fit residues: 3389.0164 Evaluate side-chains 1506 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1435 time to evaluate : 6.646 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 71 outliers final: 1 residues processed: 71 average time/residue: 0.8476 time to fit residues: 121.4430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 506 optimal weight: 6.9990 chunk 282 optimal weight: 20.0000 chunk 758 optimal weight: 10.0000 chunk 620 optimal weight: 7.9990 chunk 251 optimal weight: 2.9990 chunk 912 optimal weight: 10.0000 chunk 985 optimal weight: 30.0000 chunk 812 optimal weight: 6.9990 chunk 904 optimal weight: 30.0000 chunk 311 optimal weight: 6.9990 chunk 732 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 198 HIS B 279 ASN B 293 ASN B 319 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN G 145 ASN H 157 ASN H 162 GLN K 200 ASN K 262 ASN L 28 GLN ** L 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN N 175 ASN ** N 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 ASN O 182 ASN P 54 HIS ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 ASN ** S 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 GLN W 74 GLN ** X 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 4 GLN Y 42 GLN Y 91 ASN Z 122 HIS Z 127 ASN ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 217 GLN c 75 ASN d 21 HIS e 98 HIS ** f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 11 ASN n 165 GLN ** n 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 456 HIS ** o 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 228 ASN q 231 ASN ** r 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 49 GLN ** r 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 44 GLN t 53 ASN t 91 GLN ** t 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 230 ASN t 303 ASN u 73 GLN u 101 GLN y 6 GLN ** y 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.120 126942 Z= 0.515 Angle : 0.867 15.623 184741 Z= 0.439 Chirality : 0.046 0.305 22928 Planarity : 0.007 0.080 13136 Dihedral : 16.358 179.794 41320 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.50 % Favored : 92.31 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.34 % Twisted General : 0.24 % 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: -2.17 (0.09), residues: 7377 helix: -0.43 (0.09), residues: 2874 sheet: -1.58 (0.16), residues: 918 loop : -2.27 (0.09), residues: 3585 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1813 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1563 time to evaluate : 5.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 250 outliers final: 145 residues processed: 1700 average time/residue: 1.0694 time to fit residues: 3102.7976 Evaluate side-chains 1552 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1407 time to evaluate : 6.840 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 145 outliers final: 1 residues processed: 145 average time/residue: 0.9102 time to fit residues: 257.3035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 901 optimal weight: 10.0000 chunk 686 optimal weight: 10.0000 chunk 473 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 435 optimal weight: 9.9990 chunk 612 optimal weight: 40.0000 chunk 915 optimal weight: 7.9990 chunk 969 optimal weight: 40.0000 chunk 478 optimal weight: 0.9980 chunk 867 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 overall best weight: 3.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 184 ASN B 198 HIS ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 232 ASN K 262 ASN ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN S 62 ASN U 40 HIS V 7 GLN W 205 GLN X 94 GLN X 137 ASN Z 122 HIS Z 127 ASN ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 217 GLN ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 ASN g 33 GLN h 59 ASN j 79 GLN ** n 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 456 HIS ** o 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 10 HIS r 14 HIS r 20 HIS ** r 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 44 GLN u 42 GLN u 73 GLN ** y 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 126942 Z= 0.288 Angle : 0.701 15.842 184741 Z= 0.359 Chirality : 0.040 0.295 22928 Planarity : 0.005 0.068 13136 Dihedral : 16.061 179.878 41320 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.44 % Favored : 92.42 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.09), residues: 7377 helix: -0.09 (0.09), residues: 2874 sheet: -1.37 (0.16), residues: 926 loop : -2.10 (0.10), residues: 3577 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1787 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1616 time to evaluate : 6.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 171 outliers final: 88 residues processed: 1714 average time/residue: 1.0833 time to fit residues: 3159.6057 Evaluate side-chains 1545 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1457 time to evaluate : 5.972 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 88 outliers final: 1 residues processed: 88 average time/residue: 0.7988 time to fit residues: 140.1233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 807 optimal weight: 20.0000 chunk 550 optimal weight: 0.0070 chunk 14 optimal weight: 0.9980 chunk 721 optimal weight: 10.0000 chunk 400 optimal weight: 0.4980 chunk 827 optimal weight: 10.0000 chunk 670 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 495 optimal weight: 0.0570 chunk 870 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN C 110 ASN C 160 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 ASN F 48 ASN F 61 ASN F 225 GLN G 192 GLN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 GLN ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN N 23 GLN N 57 GLN O 42 ASN O 182 ASN ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN V 7 GLN V 98 ASN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 217 GLN ** c 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 88 HIS ** f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 83 ASN ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 11 GLN ** n 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 456 HIS ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 HIS ** r 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 44 GLN ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 837 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 126942 Z= 0.158 Angle : 0.649 16.032 184741 Z= 0.330 Chirality : 0.037 0.315 22928 Planarity : 0.005 0.072 13136 Dihedral : 15.771 179.779 41320 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.94 % Favored : 92.92 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % 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: -1.50 (0.09), residues: 7377 helix: 0.08 (0.09), residues: 2892 sheet: -1.04 (0.16), residues: 915 loop : -1.91 (0.10), residues: 3570 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1798 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1666 time to evaluate : 6.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 57 residues processed: 1732 average time/residue: 1.1857 time to fit residues: 3539.1040 Evaluate side-chains 1534 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1477 time to evaluate : 6.598 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.9690 time to fit residues: 111.4449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 326 optimal weight: 9.9990 chunk 873 optimal weight: 50.0000 chunk 191 optimal weight: 8.9990 chunk 569 optimal weight: 20.0000 chunk 239 optimal weight: 7.9990 chunk 970 optimal weight: 0.5980 chunk 805 optimal weight: 30.0000 chunk 449 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 321 optimal weight: 0.7980 chunk 509 optimal weight: 2.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 GLN E 167 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN H 5 GLN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN H 102 ASN H 162 GLN H 163 GLN K 262 ASN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 ASN L 120 GLN ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN P 116 HIS ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN V 7 GLN W 44 HIS ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 94 GLN X 137 ASN Z 122 HIS Z 127 ASN b 26 GLN b 78 HIS ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 217 GLN ** b 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 ASN l 11 GLN ** n 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 456 HIS o 103 HIS ** o 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 44 GLN ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 GLN ** y 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 126942 Z= 0.249 Angle : 0.671 15.034 184741 Z= 0.342 Chirality : 0.038 0.365 22928 Planarity : 0.005 0.071 13136 Dihedral : 15.725 179.980 41320 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.40 % Favored : 92.52 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % 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: -1.44 (0.09), residues: 7377 helix: 0.12 (0.09), residues: 2892 sheet: -1.00 (0.16), residues: 952 loop : -1.87 (0.10), residues: 3533 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1689 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1544 time to evaluate : 6.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 78 residues processed: 1621 average time/residue: 1.0700 time to fit residues: 2973.0406 Evaluate side-chains 1522 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1444 time to evaluate : 6.592 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 0 residues processed: 78 average time/residue: 0.8836 time to fit residues: 136.7006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 935 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 552 optimal weight: 7.9990 chunk 708 optimal weight: 10.0000 chunk 549 optimal weight: 2.9990 chunk 816 optimal weight: 20.0000 chunk 541 optimal weight: 0.9990 chunk 966 optimal weight: 20.0000 chunk 604 optimal weight: 0.8980 chunk 589 optimal weight: 2.9990 chunk 446 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 GLN E 138 GLN E 167 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 ASN F 225 GLN G 123 GLN H 5 GLN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN K 212 HIS ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN N 23 GLN O 182 ASN ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN U 40 HIS W 44 HIS ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 223 ASN X 94 GLN X 137 ASN Z 128 GLN b 78 HIS ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 454 GLN ** c 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 11 GLN ** n 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 183 ASN ** t 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 GLN ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 31 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 126942 Z= 0.213 Angle : 0.663 18.647 184741 Z= 0.337 Chirality : 0.038 0.572 22928 Planarity : 0.005 0.209 13136 Dihedral : 15.674 179.814 41320 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.52 % Favored : 92.37 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % 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: -1.40 (0.09), residues: 7377 helix: 0.14 (0.09), residues: 2897 sheet: -0.93 (0.16), residues: 948 loop : -1.85 (0.10), residues: 3532 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1669 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1567 time to evaluate : 6.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 53 residues processed: 1616 average time/residue: 1.1659 time to fit residues: 3237.3524 Evaluate side-chains 1515 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1462 time to evaluate : 6.575 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.9517 time to fit residues: 103.1047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 598 optimal weight: 8.9990 chunk 386 optimal weight: 3.9990 chunk 577 optimal weight: 20.0000 chunk 291 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 614 optimal weight: 0.5980 chunk 658 optimal weight: 7.9990 chunk 477 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 759 optimal weight: 20.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 GLN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 ASN ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN N 23 GLN ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN U 40 HIS V 7 GLN ** V 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS W 54 GLN X 137 ASN b 89 ASN ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 11 GLN ** n 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 92 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 126942 Z= 0.260 Angle : 0.690 16.425 184741 Z= 0.351 Chirality : 0.039 0.544 22928 Planarity : 0.005 0.087 13136 Dihedral : 15.692 180.000 41320 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.89 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.09), residues: 7377 helix: 0.19 (0.09), residues: 2890 sheet: -0.97 (0.16), residues: 958 loop : -1.84 (0.10), residues: 3529 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1608 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1515 time to evaluate : 6.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 50 residues processed: 1560 average time/residue: 1.0848 time to fit residues: 2893.1665 Evaluate side-chains 1489 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1439 time to evaluate : 6.561 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.8750 time to fit residues: 90.2010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 879 optimal weight: 30.0000 chunk 926 optimal weight: 10.0000 chunk 844 optimal weight: 20.0000 chunk 900 optimal weight: 10.0000 chunk 925 optimal weight: 8.9990 chunk 542 optimal weight: 2.9990 chunk 392 optimal weight: 1.9990 chunk 707 optimal weight: 8.9990 chunk 276 optimal weight: 5.9990 chunk 814 optimal weight: 6.9990 chunk 852 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 184 ASN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 GLN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN ** K 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN N 23 GLN N 112 ASN N 156 HIS O 182 ASN ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN U 9 GLN U 40 HIS V 98 ASN W 44 HIS X 137 ASN b 78 HIS ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 11 GLN ** n 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 456 HIS ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 GLN ** y 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 44 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.112 126942 Z= 0.422 Angle : 0.795 16.172 184741 Z= 0.403 Chirality : 0.044 0.536 22928 Planarity : 0.006 0.100 13136 Dihedral : 15.967 179.889 41320 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.16 % Favored : 90.76 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.09), residues: 7377 helix: 0.01 (0.09), residues: 2869 sheet: -1.18 (0.16), residues: 964 loop : -1.94 (0.10), residues: 3544 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1594 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1501 time to evaluate : 6.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 52 residues processed: 1539 average time/residue: 1.0934 time to fit residues: 2879.0919 Evaluate side-chains 1476 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1424 time to evaluate : 6.601 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.8350 time to fit residues: 89.7866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 897 optimal weight: 20.0000 chunk 591 optimal weight: 6.9990 chunk 952 optimal weight: 5.9990 chunk 581 optimal weight: 20.0000 chunk 451 optimal weight: 30.0000 chunk 662 optimal weight: 9.9990 chunk 999 optimal weight: 9.9990 chunk 919 optimal weight: 8.9990 chunk 795 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 614 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 GLN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN H 162 GLN ** K 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 182 ASN ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN U 40 HIS V 7 GLN ** V 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS W 54 GLN ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN ** Z 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 11 GLN ** n 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.127 126942 Z= 0.498 Angle : 0.844 17.705 184741 Z= 0.428 Chirality : 0.046 0.540 22928 Planarity : 0.006 0.078 13136 Dihedral : 16.147 179.380 41320 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.56 % Favored : 90.33 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.09), residues: 7377 helix: -0.13 (0.09), residues: 2867 sheet: -1.24 (0.16), residues: 959 loop : -2.02 (0.10), residues: 3551 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14754 Ramachandran restraints generated. 7377 Oldfield, 0 Emsley, 7377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1561 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1500 time to evaluate : 6.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 42 residues processed: 1525 average time/residue: 1.1003 time to fit residues: 2872.2471 Evaluate side-chains 1476 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1434 time to evaluate : 6.628 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.8454 time to fit residues: 76.1146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 487 optimal weight: 0.9980 chunk 632 optimal weight: 0.0070 chunk 847 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 chunk 733 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 796 optimal weight: 3.9990 chunk 333 optimal weight: 6.9990 chunk 818 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 165 GLN B 177 HIS ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 319 ASN C 260 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 GLN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN G 123 GLN ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN K 245 ASN ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN V 7 GLN ** V 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS W 54 GLN W 223 ASN Z 79 HIS ** b 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 56 ASN l 11 GLN ** n 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 42 GLN y 83 HIS ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.146153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.104385 restraints weight = 271567.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.105025 restraints weight = 206665.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106156 restraints weight = 121537.281| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 126942 Z= 0.192 Angle : 0.715 15.839 184741 Z= 0.362 Chirality : 0.039 0.535 22928 Planarity : 0.005 0.071 13136 Dihedral : 15.832 179.946 41320 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.67 % Favored : 92.21 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.21 % 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: -1.54 (0.09), residues: 7377 helix: -0.01 (0.09), residues: 2875 sheet: -1.11 (0.17), residues: 933 loop : -1.85 (0.10), residues: 3569 =============================================================================== Job complete usr+sys time: 39449.54 seconds wall clock time: 686 minutes 18.40 seconds (41178.40 seconds total)