Starting phenix.real_space_refine (version: dev) on Fri Mar 17 11:44:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpa_3535/03_2023/5mpa_3535_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpa_3535/03_2023/5mpa_3535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpa_3535/03_2023/5mpa_3535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpa_3535/03_2023/5mpa_3535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpa_3535/03_2023/5mpa_3535_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpa_3535/03_2023/5mpa_3535_updated.pdb" } resolution = 4.5 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "a TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 4": "OD1" <-> "OD2" Residue "a GLU 20": "OE1" <-> "OE2" Residue "a ASP 80": "OD1" <-> "OD2" Residue "a GLU 91": "OE1" <-> "OE2" Residue "a GLU 94": "OE1" <-> "OE2" Residue "a GLU 139": "OE1" <-> "OE2" Residue "a GLU 140": "OE1" <-> "OE2" Residue "a GLU 174": "OE1" <-> "OE2" Residue "a GLU 188": "OE1" <-> "OE2" Residue "a GLU 191": "OE1" <-> "OE2" Residue "a GLU 215": "OE1" <-> "OE2" Residue "a GLU 230": "OE1" <-> "OE2" Residue "a GLU 233": "OE1" <-> "OE2" Residue "a GLU 234": "OE1" <-> "OE2" Residue "a GLU 241": "OE1" <-> "OE2" Residue "b ASP 3": "OD1" <-> "OD2" Residue "b GLU 59": "OE1" <-> "OE2" Residue "b GLU 103": "OE1" <-> "OE2" Residue "b GLU 141": "OE1" <-> "OE2" Residue "b GLU 182": "OE1" <-> "OE2" Residue "b GLU 186": "OE1" <-> "OE2" Residue "b GLU 198": "OE1" <-> "OE2" Residue "b GLU 203": "OE1" <-> "OE2" Residue "b GLU 248": "OE1" <-> "OE2" Residue "c GLU 15": "OE1" <-> "OE2" Residue "c GLU 22": "OE1" <-> "OE2" Residue "c GLU 48": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 108": "OE1" <-> "OE2" Residue "c ARG 112": "NH1" <-> "NH2" Residue "c PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 181": "OD1" <-> "OD2" Residue "c ASP 182": "OD1" <-> "OD2" Residue "c GLU 190": "OE1" <-> "OE2" Residue "c GLU 223": "OE1" <-> "OE2" Residue "c GLU 233": "OE1" <-> "OE2" Residue "d GLU 19": "OE1" <-> "OE2" Residue "d PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 105": "OE1" <-> "OE2" Residue "d ARG 109": "NH1" <-> "NH2" Residue "d PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 142": "OE1" <-> "OE2" Residue "d TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 164": "NH1" <-> "NH2" Residue "d GLU 171": "OE1" <-> "OE2" Residue "d GLU 188": "OE1" <-> "OE2" Residue "d GLU 199": "OE1" <-> "OE2" Residue "d GLU 226": "OE1" <-> "OE2" Residue "e GLU 10": "OE1" <-> "OE2" Residue "e GLU 17": "OE1" <-> "OE2" Residue "e GLU 21": "OE1" <-> "OE2" Residue "e GLU 43": "OE1" <-> "OE2" Residue "e GLU 52": "OE1" <-> "OE2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "e ARG 64": "NH1" <-> "NH2" Residue "e ASP 110": "OD1" <-> "OD2" Residue "e GLU 117": "OE1" <-> "OE2" Residue "e TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 169": "OE1" <-> "OE2" Residue "e GLU 178": "OE1" <-> "OE2" Residue "e GLU 187": "OE1" <-> "OE2" Residue "e GLU 189": "OE1" <-> "OE2" Residue "e GLU 230": "OE1" <-> "OE2" Residue "e GLU 237": "OE1" <-> "OE2" Residue "e GLU 239": "OE1" <-> "OE2" Residue "f GLU 22": "OE1" <-> "OE2" Residue "f GLU 26": "OE1" <-> "OE2" Residue "f GLU 54": "OE1" <-> "OE2" Residue "f GLU 67": "OE1" <-> "OE2" Residue "f PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 145": "OE1" <-> "OE2" Residue "f PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 154": "OE1" <-> "OE2" Residue "f GLU 187": "OE1" <-> "OE2" Residue "f GLU 194": "OE1" <-> "OE2" Residue "f GLU 203": "OE1" <-> "OE2" Residue "g GLU 21": "OE1" <-> "OE2" Residue "g GLU 28": "OE1" <-> "OE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 148": "OE1" <-> "OE2" Residue "g TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 173": "OE1" <-> "OE2" Residue "g GLU 181": "OE1" <-> "OE2" Residue "g GLU 209": "OE1" <-> "OE2" Residue "g GLU 211": "OE1" <-> "OE2" Residue "g ASP 230": "OD1" <-> "OD2" Residue "g GLU 234": "OE1" <-> "OE2" Residue "g GLU 242": "OE1" <-> "OE2" Residue "h PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 84": "OE1" <-> "OE2" Residue "h GLU 88": "OE1" <-> "OE2" Residue "h TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 149": "OE1" <-> "OE2" Residue "h PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 184": "OE1" <-> "OE2" Residue "i ASP 28": "OD1" <-> "OD2" Residue "i TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 139": "OE1" <-> "OE2" Residue "i ASP 145": "OD1" <-> "OD2" Residue "i GLU 149": "OE1" <-> "OE2" Residue "i GLU 150": "OE1" <-> "OE2" Residue "i GLU 185": "OE1" <-> "OE2" Residue "i GLU 197": "OE1" <-> "OE2" Residue "i GLU 225": "OE1" <-> "OE2" Residue "i GLU 226": "OE1" <-> "OE2" Residue "j ASP 2": "OD1" <-> "OD2" Residue "j GLU 40": "OE1" <-> "OE2" Residue "j GLU 64": "OE1" <-> "OE2" Residue "j GLU 78": "OE1" <-> "OE2" Residue "j ARG 98": "NH1" <-> "NH2" Residue "j PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 158": "OE1" <-> "OE2" Residue "j GLU 160": "OE1" <-> "OE2" Residue "j GLU 164": "OE1" <-> "OE2" Residue "j GLU 193": "OE1" <-> "OE2" Residue "j ASP 204": "OD1" <-> "OD2" Residue "k ARG 23": "NH1" <-> "NH2" Residue "k GLU 49": "OE1" <-> "OE2" Residue "k ASP 52": "OD1" <-> "OD2" Residue "k GLU 58": "OE1" <-> "OE2" Residue "k TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 71": "OE1" <-> "OE2" Residue "k GLU 74": "OE1" <-> "OE2" Residue "k GLU 115": "OE1" <-> "OE2" Residue "k ASP 145": "OD1" <-> "OD2" Residue "k GLU 155": "OE1" <-> "OE2" Residue "k GLU 156": "OE1" <-> "OE2" Residue "k GLU 167": "OE1" <-> "OE2" Residue "l GLU 36": "OE1" <-> "OE2" Residue "l GLU 56": "OE1" <-> "OE2" Residue "l GLU 67": "OE1" <-> "OE2" Residue "l GLU 70": "OE1" <-> "OE2" Residue "l ARG 121": "NH1" <-> "NH2" Residue "l GLU 182": "OE1" <-> "OE2" Residue "l GLU 195": "OE1" <-> "OE2" Residue "l GLU 202": "OE1" <-> "OE2" Residue "l GLU 204": "OE1" <-> "OE2" Residue "m GLU 18": "OE1" <-> "OE2" Residue "m PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 26": "OD1" <-> "OD2" Residue "m ARG 28": "NH1" <-> "NH2" Residue "m GLU 40": "OE1" <-> "OE2" Residue "m TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 116": "OE1" <-> "OE2" Residue "m PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 132": "OE1" <-> "OE2" Residue "m GLU 134": "OE1" <-> "OE2" Residue "m GLU 161": "OE1" <-> "OE2" Residue "m GLU 193": "OE1" <-> "OE2" Residue "m GLU 215": "OE1" <-> "OE2" Residue "m GLU 218": "OE1" <-> "OE2" Residue "n GLU 40": "OE1" <-> "OE2" Residue "n GLU 64": "OE1" <-> "OE2" Residue "n GLU 85": "OE1" <-> "OE2" Residue "n GLU 94": "OE1" <-> "OE2" Residue "n TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 162": "OE1" <-> "OE2" Residue "n ARG 182": "NH1" <-> "NH2" Residue "n TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 215": "OE1" <-> "OE2" Residue "A TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "B ASP 3": "OD1" <-> "OD2" Residue "B PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 151": "OD1" <-> "OD2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "D PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 181": "OE1" <-> "OE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "G PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 166": "OD1" <-> "OD2" Residue "1 GLU 192": "OE1" <-> "OE2" Residue "2 PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 179": "OE1" <-> "OE2" Residue "2 GLU 197": "OE1" <-> "OE2" Residue "2 GLU 198": "OE1" <-> "OE2" Residue "2 TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 222": "OD1" <-> "OD2" Residue "3 PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 98": "NH1" <-> "NH2" Residue "3 GLU 193": "OE1" <-> "OE2" Residue "4 ARG 23": "NH1" <-> "NH2" Residue "4 TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 67": "OE1" <-> "OE2" Residue "5 GLU 72": "OE1" <-> "OE2" Residue "5 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 182": "OE1" <-> "OE2" Residue "6 TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 203": "OE1" <-> "OE2" Residue "6 GLU 215": "OE1" <-> "OE2" Residue "7 ASP 25": "OD1" <-> "OD2" Residue "7 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 64": "OE1" <-> "OE2" Residue "7 GLU 73": "OE1" <-> "OE2" Residue "7 TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 162": "OE1" <-> "OE2" Residue "7 PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 215": "OE1" <-> "OE2" Residue "7 PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 177": "OD1" <-> "OD2" Residue "H GLU 202": "OE1" <-> "OE2" Residue "H GLU 219": "OE1" <-> "OE2" Residue "H PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 293": "OE1" <-> "OE2" Residue "H GLU 310": "OE1" <-> "OE2" Residue "H PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 372": "OD1" <-> "OD2" Residue "H GLU 405": "OE1" <-> "OE2" Residue "H PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "I PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "I TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "I GLU 193": "OE1" <-> "OE2" Residue "I GLU 210": "OE1" <-> "OE2" Residue "I GLU 273": "OE1" <-> "OE2" Residue "I GLU 299": "OE1" <-> "OE2" Residue "I ASP 354": "OD1" <-> "OD2" Residue "I ASP 386": "OD1" <-> "OD2" Residue "K TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 291": "OE1" <-> "OE2" Residue "K GLU 365": "OE1" <-> "OE2" Residue "L TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "L TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 274": "OE1" <-> "OE2" Residue "L GLU 354": "OE1" <-> "OE2" Residue "L PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 397": "OE1" <-> "OE2" Residue "L GLU 429": "OE1" <-> "OE2" Residue "M GLU 29": "OE1" <-> "OE2" Residue "M TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 162": "OE1" <-> "OE2" Residue "M GLU 174": "OE1" <-> "OE2" Residue "M TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 258": "OE1" <-> "OE2" Residue "M GLU 272": "OE1" <-> "OE2" Residue "M GLU 282": "OE1" <-> "OE2" Residue "M GLU 300": "OE1" <-> "OE2" Residue "M ARG 425": "NH1" <-> "NH2" Residue "J GLU 16": "OE1" <-> "OE2" Residue "J TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 232": "OE1" <-> "OE2" Residue "J GLU 249": "OE1" <-> "OE2" Residue "J ARG 306": "NH1" <-> "NH2" Residue "J GLU 348": "OE1" <-> "OE2" Residue "J GLU 395": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 67883 Number of models: 1 Model: "" Number of chains: 40 Chain: "a" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1907 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "b" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1915 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain: "c" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1904 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "d" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1881 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 10, 'TRANS': 229} Chain: "e" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1861 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "f" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1773 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain: "g" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1892 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "h" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1512 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "i" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1719 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "j" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1581 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "k" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1561 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "l" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1644 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain: "m" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1757 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "n" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1815 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 8, 'TRANS': 223} Chain: "A" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1907 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1915 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain: "C" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1904 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "D" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1881 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 10, 'TRANS': 229} Chain: "E" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1861 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "F" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1795 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain: "G" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1892 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "1" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1512 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "2" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1719 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "3" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1581 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "4" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1561 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "5" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1644 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain: "6" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1757 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "7" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1790 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "H" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3053 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 368} Chain breaks: 1 Chain: "I" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3022 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 367} Chain: "K" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3078 Classifications: {'peptide': 389} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 371} Chain: "L" Number of atoms: 3082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3082 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 370} Chain: "M" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2986 Classifications: {'peptide': 381} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 365} Chain breaks: 1 Chain: "J" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3033 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 369} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 27.48, per 1000 atoms: 0.40 Number of scatterers: 67883 At special positions: 0 Unit cell: (291.18, 189.06, 175.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 245 16.00 P 17 15.00 Mg 6 11.99 O 13176 8.00 N 11637 7.00 C 42802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM67720 O3A ATP H 502 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.70 Conformation dependent library (CDL) restraints added in 7.3 seconds 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16006 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 242 helices and 81 sheets defined 35.8% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'a' and resid 3 through 5 No H-bonds generated for 'chain 'a' and resid 3 through 5' Processing helix chain 'a' and resid 17 through 26 removed outlier: 3.747A pdb=" N PHE a 23 " --> pdb=" O VAL a 19 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 78 through 98 removed outlier: 3.509A pdb=" N ARG a 96 " --> pdb=" O ALA a 92 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 121 removed outlier: 3.848A pdb=" N TYR a 119 " --> pdb=" O LEU a 115 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR a 120 " --> pdb=" O SER a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 180 removed outlier: 4.511A pdb=" N GLN a 167 " --> pdb=" O PRO a 164 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU a 168 " --> pdb=" O LYS a 165 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR a 170 " --> pdb=" O GLN a 167 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR a 171 " --> pdb=" O GLU a 168 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE a 177 " --> pdb=" O GLU a 174 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS a 178 " --> pdb=" O ASN a 175 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER a 180 " --> pdb=" O PHE a 177 " (cutoff:3.500A) Processing helix chain 'a' and resid 190 through 205 Processing helix chain 'a' and resid 229 through 241 removed outlier: 3.526A pdb=" N ALA a 238 " --> pdb=" O GLU a 234 " (cutoff:3.500A) Processing helix chain 'b' and resid 19 through 30 removed outlier: 3.625A pdb=" N TYR b 23 " --> pdb=" O GLY b 19 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU b 25 " --> pdb=" O ILE b 21 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR b 26 " --> pdb=" O ASP b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 79 through 95 removed outlier: 3.678A pdb=" N ARG b 83 " --> pdb=" O GLY b 79 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 123 removed outlier: 3.626A pdb=" N VAL b 111 " --> pdb=" O THR b 107 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER b 112 " --> pdb=" O LYS b 108 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR b 122 " --> pdb=" O MET b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 168 through 178 removed outlier: 3.667A pdb=" N LYS b 177 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG b 178 " --> pdb=" O PHE b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 185 through 198 removed outlier: 3.636A pdb=" N LEU b 193 " --> pdb=" O ILE b 189 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU b 194 " --> pdb=" O HIS b 190 " (cutoff:3.500A) Processing helix chain 'b' and resid 240 through 246 removed outlier: 3.606A pdb=" N ASN b 244 " --> pdb=" O SER b 240 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP b 245 " --> pdb=" O GLN b 241 " (cutoff:3.500A) Processing helix chain 'c' and resid 3 through 5 No H-bonds generated for 'chain 'c' and resid 3 through 5' Processing helix chain 'c' and resid 19 through 30 Processing helix chain 'c' and resid 80 through 101 removed outlier: 4.009A pdb=" N ILE c 85 " --> pdb=" O ALA c 81 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 121 removed outlier: 3.729A pdb=" N ASP c 116 " --> pdb=" O ARG c 112 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR c 121 " --> pdb=" O ILE c 117 " (cutoff:3.500A) Processing helix chain 'c' and resid 168 through 178 removed outlier: 3.744A pdb=" N LEU c 174 " --> pdb=" O ALA c 170 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET c 177 " --> pdb=" O THR c 173 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP c 178 " --> pdb=" O LEU c 174 " (cutoff:3.500A) Processing helix chain 'c' and resid 185 through 199 removed outlier: 3.701A pdb=" N THR c 195 " --> pdb=" O LEU c 191 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU c 196 " --> pdb=" O ALA c 192 " (cutoff:3.500A) Processing helix chain 'c' and resid 234 through 240 Processing helix chain 'd' and resid 16 through 27 Processing helix chain 'd' and resid 77 through 98 removed outlier: 3.630A pdb=" N ARG d 81 " --> pdb=" O ASN d 77 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU d 83 " --> pdb=" O ASP d 79 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA d 87 " --> pdb=" O LEU d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 104 through 119 removed outlier: 3.659A pdb=" N TYR d 118 " --> pdb=" O VAL d 114 " (cutoff:3.500A) Processing helix chain 'd' and resid 168 through 176 removed outlier: 3.842A pdb=" N PHE d 172 " --> pdb=" O THR d 168 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 197 Processing helix chain 'd' and resid 224 through 238 removed outlier: 3.504A pdb=" N THR d 232 " --> pdb=" O ASN d 228 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN d 233 " --> pdb=" O GLN d 229 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN d 236 " --> pdb=" O THR d 232 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU d 237 " --> pdb=" O GLN d 233 " (cutoff:3.500A) Processing helix chain 'e' and resid 14 through 25 removed outlier: 3.745A pdb=" N GLU e 21 " --> pdb=" O GLU e 17 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA e 22 " --> pdb=" O TYR e 18 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE e 23 " --> pdb=" O SER e 19 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS e 24 " --> pdb=" O LEU e 20 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU e 25 " --> pdb=" O GLU e 21 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 94 removed outlier: 3.682A pdb=" N ARG e 78 " --> pdb=" O THR e 74 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER e 79 " --> pdb=" O ALA e 75 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET e 80 " --> pdb=" O ASP e 76 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU e 82 " --> pdb=" O ARG e 78 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 113 removed outlier: 3.984A pdb=" N LEU e 111 " --> pdb=" O SER e 107 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA e 112 " --> pdb=" O VAL e 108 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU e 113 " --> pdb=" O CYS e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 168 through 178 removed outlier: 4.371A pdb=" N ASN e 177 " --> pdb=" O ALA e 173 " (cutoff:3.500A) Processing helix chain 'e' and resid 185 through 199 removed outlier: 3.869A pdb=" N LEU e 190 " --> pdb=" O LYS e 186 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL e 199 " --> pdb=" O ILE e 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 225 through 240 removed outlier: 3.518A pdb=" N ALA e 229 " --> pdb=" O ASN e 225 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU e 230 " --> pdb=" O GLU e 226 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU e 231 " --> pdb=" O LYS e 227 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS e 233 " --> pdb=" O ALA e 229 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU e 237 " --> pdb=" O LYS e 233 " (cutoff:3.500A) Processing helix chain 'f' and resid 19 through 28 removed outlier: 3.633A pdb=" N ILE f 28 " --> pdb=" O ALA f 24 " (cutoff:3.500A) Processing helix chain 'f' and resid 77 through 98 removed outlier: 3.500A pdb=" N ARG f 81 " --> pdb=" O ALA f 77 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL f 82 " --> pdb=" O PRO f 78 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 120 removed outlier: 3.677A pdb=" N GLY f 108 " --> pdb=" O VAL f 104 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N HIS f 109 " --> pdb=" O GLU f 105 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU f 110 " --> pdb=" O ARG f 106 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS f 114 " --> pdb=" O LEU f 110 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN f 118 " --> pdb=" O LYS f 114 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR f 119 " --> pdb=" O ALA f 115 " (cutoff:3.500A) Processing helix chain 'f' and resid 164 through 173 removed outlier: 3.875A pdb=" N THR f 169 " --> pdb=" O GLY f 166 " (cutoff:3.500A) Processing helix chain 'f' and resid 175 through 180 removed outlier: 4.187A pdb=" N LYS f 180 " --> pdb=" O ASP f 176 " (cutoff:3.500A) Processing helix chain 'f' and resid 185 through 199 removed outlier: 3.707A pdb=" N GLY f 192 " --> pdb=" O LEU f 188 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN f 198 " --> pdb=" O GLU f 194 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER f 199 " --> pdb=" O ALA f 195 " (cutoff:3.500A) Processing helix chain 'f' and resid 226 through 229 removed outlier: 3.945A pdb=" N VAL f 229 " --> pdb=" O GLY f 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 226 through 229' Processing helix chain 'g' and resid 18 through 28 removed outlier: 3.846A pdb=" N LYS g 25 " --> pdb=" O GLU g 21 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA g 26 " --> pdb=" O TYR g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 78 through 98 removed outlier: 3.512A pdb=" N GLU g 90 " --> pdb=" O ASN g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 105 through 120 removed outlier: 3.695A pdb=" N ASP g 110 " --> pdb=" O PRO g 106 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS g 119 " --> pdb=" O TYR g 115 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR g 120 " --> pdb=" O VAL g 116 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 177 Processing helix chain 'g' and resid 185 through 201 removed outlier: 3.792A pdb=" N VAL g 189 " --> pdb=" O ALA g 185 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS g 190 " --> pdb=" O ARG g 186 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU g 201 " --> pdb=" O TYR g 197 " (cutoff:3.500A) Processing helix chain 'g' and resid 229 through 240 removed outlier: 3.619A pdb=" N ALA g 239 " --> pdb=" O ALA g 235 " (cutoff:3.500A) Processing helix chain 'h' and resid 49 through 70 removed outlier: 3.613A pdb=" N ILE h 55 " --> pdb=" O ASP h 51 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP h 57 " --> pdb=" O GLN h 53 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN h 60 " --> pdb=" O ALA h 56 " (cutoff:3.500A) Processing helix chain 'h' and resid 75 through 86 removed outlier: 3.531A pdb=" N PHE h 82 " --> pdb=" O ALA h 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 131 through 141 removed outlier: 3.738A pdb=" N TYR h 135 " --> pdb=" O THR h 132 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLY h 136 " --> pdb=" O PHE h 133 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR h 137 " --> pdb=" O ILE h 134 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS h 138 " --> pdb=" O TYR h 135 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP h 139 " --> pdb=" O GLY h 136 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS h 140 " --> pdb=" O TYR h 137 " (cutoff:3.500A) Processing helix chain 'h' and resid 148 through 165 removed outlier: 3.540A pdb=" N TRP h 165 " --> pdb=" O GLN h 161 " (cutoff:3.500A) Processing helix chain 'h' and resid 190 through 192 No H-bonds generated for 'chain 'h' and resid 190 through 192' Processing helix chain 'i' and resid 49 through 70 removed outlier: 3.630A pdb=" N VAL i 55 " --> pdb=" O ASP i 51 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN i 62 " --> pdb=" O LEU i 58 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU i 68 " --> pdb=" O GLU i 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR i 69 " --> pdb=" O LEU i 65 " (cutoff:3.500A) Processing helix chain 'i' and resid 76 through 90 removed outlier: 4.080A pdb=" N TYR i 90 " --> pdb=" O HIS i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 132 through 141 removed outlier: 3.719A pdb=" N VAL i 137 " --> pdb=" O ALA i 133 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER i 140 " --> pdb=" O ALA i 136 " (cutoff:3.500A) Processing helix chain 'i' and resid 148 through 165 removed outlier: 3.890A pdb=" N LYS i 153 " --> pdb=" O GLU i 149 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 77 removed outlier: 3.904A pdb=" N THR j 60 " --> pdb=" O ALA j 56 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE j 66 " --> pdb=" O LEU j 62 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU j 72 " --> pdb=" O TYR j 68 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 96 removed outlier: 4.032A pdb=" N GLN j 88 " --> pdb=" O GLU j 84 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU j 96 " --> pdb=" O SER j 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 142 through 152 removed outlier: 3.636A pdb=" N GLY j 147 " --> pdb=" O ASP j 143 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET j 148 " --> pdb=" O GLN j 144 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU j 150 " --> pdb=" O PHE j 146 " (cutoff:3.500A) Processing helix chain 'j' and resid 162 through 175 removed outlier: 3.987A pdb=" N SER j 167 " --> pdb=" O PHE j 163 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA j 173 " --> pdb=" O ALA j 169 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA j 174 " --> pdb=" O LEU j 170 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP j 175 " --> pdb=" O LEU j 171 " (cutoff:3.500A) Processing helix chain 'k' and resid 52 through 71 removed outlier: 3.508A pdb=" N ALA k 57 " --> pdb=" O THR k 53 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE k 60 " --> pdb=" O PHE k 56 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN k 63 " --> pdb=" O TYR k 59 " (cutoff:3.500A) Processing helix chain 'k' and resid 77 through 93 removed outlier: 3.870A pdb=" N SER k 82 " --> pdb=" O GLN k 78 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU k 87 " --> pdb=" O PHE k 83 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE k 92 " --> pdb=" O LEU k 88 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG k 93 " --> pdb=" O ALA k 89 " (cutoff:3.500A) Processing helix chain 'k' and resid 136 through 140 Processing helix chain 'k' and resid 143 through 147 removed outlier: 3.810A pdb=" N HIS k 147 " --> pdb=" O LEU k 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 143 through 147' Processing helix chain 'k' and resid 154 through 171 removed outlier: 3.608A pdb=" N ASP k 159 " --> pdb=" O GLU k 155 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU k 163 " --> pdb=" O ASP k 159 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN k 166 " --> pdb=" O LYS k 162 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS k 170 " --> pdb=" O GLN k 166 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG k 171 " --> pdb=" O GLU k 167 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 70 removed outlier: 3.577A pdb=" N THR l 57 " --> pdb=" O GLN l 53 " (cutoff:3.500A) Processing helix chain 'l' and resid 76 through 90 removed outlier: 3.653A pdb=" N LEU l 83 " --> pdb=" O ALA l 79 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN l 85 " --> pdb=" O LYS l 81 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN l 89 " --> pdb=" O ASN l 85 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR l 90 " --> pdb=" O LEU l 86 " (cutoff:3.500A) Processing helix chain 'l' and resid 133 through 141 removed outlier: 3.505A pdb=" N GLY l 138 " --> pdb=" O THR l 134 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL l 139 " --> pdb=" O PHE l 135 " (cutoff:3.500A) Processing helix chain 'l' and resid 150 through 167 removed outlier: 3.544A pdb=" N SER l 160 " --> pdb=" O LEU l 156 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS l 166 " --> pdb=" O LEU l 162 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG l 167 " --> pdb=" O ALA l 163 " (cutoff:3.500A) Processing helix chain 'l' and resid 193 through 204 removed outlier: 4.375A pdb=" N TRP l 198 " --> pdb=" O GLY l 194 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS l 199 " --> pdb=" O GLU l 195 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU l 202 " --> pdb=" O TRP l 198 " (cutoff:3.500A) Processing helix chain 'm' and resid 58 through 78 removed outlier: 3.772A pdb=" N ALA m 63 " --> pdb=" O ALA m 59 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG m 67 " --> pdb=" O ALA m 63 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS m 73 " --> pdb=" O LYS m 69 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR m 75 " --> pdb=" O SER m 71 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP m 78 " --> pdb=" O TRP m 74 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 102 removed outlier: 3.621A pdb=" N ARG m 91 " --> pdb=" O ASN m 87 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN m 94 " --> pdb=" O ALA m 90 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS m 95 " --> pdb=" O ARG m 91 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS m 100 " --> pdb=" O LEU m 96 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG m 101 " --> pdb=" O LEU m 97 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N PHE m 102 " --> pdb=" O TYR m 98 " (cutoff:3.500A) Processing helix chain 'm' and resid 143 through 154 Proline residue: m 148 - end of helix Processing helix chain 'm' and resid 177 through 194 removed outlier: 3.676A pdb=" N GLU m 193 " --> pdb=" O THR m 189 " (cutoff:3.500A) Processing helix chain 'n' and resid 57 through 75 removed outlier: 4.363A pdb=" N LEU n 66 " --> pdb=" O HIS n 62 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR n 72 " --> pdb=" O LYS n 68 " (cutoff:3.500A) Processing helix chain 'n' and resid 89 through 105 removed outlier: 3.839A pdb=" N GLU n 94 " --> pdb=" O SER n 90 " (cutoff:3.500A) Processing helix chain 'n' and resid 145 through 148 Processing helix chain 'n' and resid 152 through 158 removed outlier: 3.794A pdb=" N VAL n 158 " --> pdb=" O LEU n 154 " (cutoff:3.500A) Processing helix chain 'n' and resid 162 through 164 No H-bonds generated for 'chain 'n' and resid 162 through 164' Processing helix chain 'n' and resid 170 through 187 removed outlier: 3.624A pdb=" N GLU n 174 " --> pdb=" O VAL n 170 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU n 175 " --> pdb=" O GLN n 171 " (cutoff:3.500A) Processing helix chain 'n' and resid 221 through 223 No H-bonds generated for 'chain 'n' and resid 221 through 223' Processing helix chain 'A' and resid 3 through 6 No H-bonds generated for 'chain 'A' and resid 3 through 6' Processing helix chain 'A' and resid 17 through 25 removed outlier: 3.849A pdb=" N ALA A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 99 removed outlier: 3.953A pdb=" N ASN A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.577A pdb=" N THR A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 3.516A pdb=" N THR A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 205 removed outlier: 3.597A pdb=" N VAL A 194 " --> pdb=" O TRP A 190 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 204 " --> pdb=" O HIS A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 240 removed outlier: 3.530A pdb=" N ALA A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.548A pdb=" N LEU B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 97 removed outlier: 3.522A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 removed outlier: 3.606A pdb=" N ILE B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 removed outlier: 3.948A pdb=" N LYS B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 199 removed outlier: 3.523A pdb=" N GLU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 246 Processing helix chain 'C' and resid 2 through 5 No H-bonds generated for 'chain 'C' and resid 2 through 5' Processing helix chain 'C' and resid 19 through 29 removed outlier: 3.567A pdb=" N ILE C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 101 removed outlier: 3.796A pdb=" N ILE C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.663A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.506A pdb=" N MET C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 removed outlier: 3.625A pdb=" N LYS C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'D' and resid 16 through 27 removed outlier: 3.667A pdb=" N LYS D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 98 removed outlier: 4.330A pdb=" N ARG D 81 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.573A pdb=" N TYR D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 removed outlier: 4.078A pdb=" N LYS D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 199 removed outlier: 3.916A pdb=" N GLU D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 239 Processing helix chain 'E' and resid 14 through 25 removed outlier: 3.714A pdb=" N GLU E 21 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA E 22 " --> pdb=" O TYR E 18 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 76 through 94 removed outlier: 4.115A pdb=" N MET E 80 " --> pdb=" O ASP E 76 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 82 " --> pdb=" O ARG E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 168 through 178 removed outlier: 3.828A pdb=" N ASN E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 198 removed outlier: 3.824A pdb=" N LEU E 190 " --> pdb=" O LYS E 186 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 241 removed outlier: 3.508A pdb=" N ALA E 229 " --> pdb=" O ASN E 225 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU E 237 " --> pdb=" O LYS E 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 30 removed outlier: 3.932A pdb=" N ILE F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN F 30 " --> pdb=" O GLU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 96 removed outlier: 3.593A pdb=" N ARG F 81 " --> pdb=" O ALA F 77 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL F 82 " --> pdb=" O PRO F 78 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN F 85 " --> pdb=" O ARG F 81 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER F 95 " --> pdb=" O CYS F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 120 removed outlier: 3.602A pdb=" N HIS F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR F 119 " --> pdb=" O ALA F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 173 removed outlier: 4.309A pdb=" N THR F 169 " --> pdb=" O GLY F 166 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 171 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 185 through 196 removed outlier: 3.514A pdb=" N ILE F 189 " --> pdb=" O PRO F 185 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 4.257A pdb=" N TYR F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 29 removed outlier: 4.155A pdb=" N LYS G 25 " --> pdb=" O GLU G 21 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA G 26 " --> pdb=" O TYR G 22 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU G 28 " --> pdb=" O VAL G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 99 removed outlier: 3.661A pdb=" N ARG G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU G 84 " --> pdb=" O ASP G 80 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG G 89 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU G 98 " --> pdb=" O SER G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 120 removed outlier: 3.904A pdb=" N VAL G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA G 118 " --> pdb=" O GLN G 114 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS G 119 " --> pdb=" O TYR G 115 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR G 120 " --> pdb=" O VAL G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 177 removed outlier: 4.037A pdb=" N GLU G 171 " --> pdb=" O SER G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 198 removed outlier: 4.662A pdb=" N LYS G 190 " --> pdb=" O ARG G 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE G 195 " --> pdb=" O GLN G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 242 removed outlier: 3.751A pdb=" N ALA G 235 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE G 238 " --> pdb=" O GLU G 234 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA G 239 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU G 242 " --> pdb=" O PHE G 238 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 67 removed outlier: 3.655A pdb=" N ILE 1 58 " --> pdb=" O ALA 1 54 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU 1 65 " --> pdb=" O TYR 1 61 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 88 removed outlier: 3.507A pdb=" N GLU 1 84 " --> pdb=" O SER 1 80 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU 1 88 " --> pdb=" O GLU 1 84 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 132 No H-bonds generated for 'chain '1' and resid 130 through 132' Processing helix chain '1' and resid 135 through 141 removed outlier: 3.784A pdb=" N ASN 1 141 " --> pdb=" O TYR 1 137 " (cutoff:3.500A) Processing helix chain '1' and resid 148 through 165 removed outlier: 3.520A pdb=" N ALA 1 162 " --> pdb=" O SER 1 158 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 195 removed outlier: 4.390A pdb=" N GLN 1 195 " --> pdb=" O ASP 1 191 " (cutoff:3.500A) Processing helix chain '2' and resid 49 through 70 removed outlier: 3.543A pdb=" N ASN 2 62 " --> pdb=" O LEU 2 58 " (cutoff:3.500A) Processing helix chain '2' and resid 76 through 89 removed outlier: 3.667A pdb=" N HIS 2 86 " --> pdb=" O MET 2 82 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS 2 89 " --> pdb=" O GLN 2 85 " (cutoff:3.500A) Processing helix chain '2' and resid 131 through 141 removed outlier: 4.626A pdb=" N VAL 2 137 " --> pdb=" O ALA 2 133 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER 2 140 " --> pdb=" O ALA 2 136 " (cutoff:3.500A) Processing helix chain '2' and resid 148 through 165 removed outlier: 3.673A pdb=" N ILE 2 152 " --> pdb=" O LYS 2 148 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS 2 153 " --> pdb=" O GLU 2 149 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP 2 164 " --> pdb=" O GLN 2 160 " (cutoff:3.500A) Processing helix chain '3' and resid 4 through 7 No H-bonds generated for 'chain '3' and resid 4 through 7' Processing helix chain '3' and resid 56 through 77 removed outlier: 3.588A pdb=" N THR 3 60 " --> pdb=" O ALA 3 56 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS 3 76 " --> pdb=" O LEU 3 72 " (cutoff:3.500A) Processing helix chain '3' and resid 83 through 97 removed outlier: 3.995A pdb=" N ARG 3 97 " --> pdb=" O SER 3 93 " (cutoff:3.500A) Processing helix chain '3' and resid 142 through 152 removed outlier: 3.661A pdb=" N GLY 3 147 " --> pdb=" O ASP 3 143 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET 3 148 " --> pdb=" O GLN 3 144 " (cutoff:3.500A) Processing helix chain '3' and resid 159 through 176 removed outlier: 3.757A pdb=" N PHE 3 163 " --> pdb=" O PRO 3 159 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU 3 164 " --> pdb=" O GLU 3 160 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA 3 173 " --> pdb=" O ALA 3 169 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP 3 175 " --> pdb=" O LEU 3 171 " (cutoff:3.500A) Processing helix chain '4' and resid 52 through 71 removed outlier: 3.993A pdb=" N ILE 4 60 " --> pdb=" O PHE 4 56 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER 4 68 " --> pdb=" O ILE 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 77 through 93 removed outlier: 3.808A pdb=" N SER 4 82 " --> pdb=" O GLN 4 78 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG 4 93 " --> pdb=" O ALA 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 136 through 147 removed outlier: 3.851A pdb=" N THR 4 140 " --> pdb=" O GLY 4 137 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER 4 142 " --> pdb=" O TYR 4 139 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP 4 145 " --> pdb=" O SER 4 142 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS 4 146 " --> pdb=" O LEU 4 143 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS 4 147 " --> pdb=" O LEU 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 154 through 171 removed outlier: 3.674A pdb=" N LYS 4 170 " --> pdb=" O GLN 4 166 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 67 removed outlier: 3.882A pdb=" N TRP 5 55 " --> pdb=" O ASP 5 51 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU 5 56 " --> pdb=" O CYS 5 52 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN 5 62 " --> pdb=" O TRP 5 58 " (cutoff:3.500A) Processing helix chain '5' and resid 76 through 89 removed outlier: 3.896A pdb=" N GLN 5 89 " --> pdb=" O ASN 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 131 through 142 removed outlier: 4.648A pdb=" N THR 5 134 " --> pdb=" O SER 5 131 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE 5 135 " --> pdb=" O GLY 5 132 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA 5 136 " --> pdb=" O GLN 5 133 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR 5 137 " --> pdb=" O THR 5 134 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL 5 139 " --> pdb=" O ALA 5 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP 5 141 " --> pdb=" O GLY 5 138 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER 5 142 " --> pdb=" O VAL 5 139 " (cutoff:3.500A) Processing helix chain '5' and resid 150 through 167 removed outlier: 3.502A pdb=" N ARG 5 159 " --> pdb=" O TYR 5 155 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG 5 167 " --> pdb=" O ALA 5 163 " (cutoff:3.500A) Processing helix chain '5' and resid 193 through 202 removed outlier: 4.349A pdb=" N TRP 5 198 " --> pdb=" O GLY 5 194 " (cutoff:3.500A) Processing helix chain '6' and resid 58 through 78 removed outlier: 3.949A pdb=" N ALA 6 63 " --> pdb=" O ALA 6 59 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG 6 67 " --> pdb=" O ALA 6 63 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE 6 68 " --> pdb=" O LEU 6 64 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS 6 76 " --> pdb=" O VAL 6 72 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE 6 77 " --> pdb=" O LYS 6 73 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP 6 78 " --> pdb=" O TRP 6 74 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 100 removed outlier: 3.655A pdb=" N ARG 6 91 " --> pdb=" O ASN 6 87 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS 6 95 " --> pdb=" O ARG 6 91 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS 6 100 " --> pdb=" O LEU 6 96 " (cutoff:3.500A) Processing helix chain '6' and resid 143 through 153 Proline residue: 6 148 - end of helix removed outlier: 3.648A pdb=" N ASP 6 151 " --> pdb=" O MET 6 147 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN 6 152 " --> pdb=" O PRO 6 148 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN 6 153 " --> pdb=" O PHE 6 149 " (cutoff:3.500A) Processing helix chain '6' and resid 177 through 194 removed outlier: 3.678A pdb=" N LYS 6 182 " --> pdb=" O GLU 6 178 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR 6 192 " --> pdb=" O PHE 6 188 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU 6 193 " --> pdb=" O THR 6 189 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG 6 194 " --> pdb=" O SER 6 190 " (cutoff:3.500A) Processing helix chain '7' and resid 57 through 75 removed outlier: 3.678A pdb=" N HIS 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU 7 66 " --> pdb=" O HIS 7 62 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU 7 67 " --> pdb=" O ILE 7 63 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS 7 68 " --> pdb=" O GLU 7 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR 7 72 " --> pdb=" O LYS 7 68 " (cutoff:3.500A) Processing helix chain '7' and resid 89 through 105 removed outlier: 3.504A pdb=" N GLU 7 94 " --> pdb=" O SER 7 90 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN 7 102 " --> pdb=" O THR 7 98 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG 7 104 " --> pdb=" O MET 7 100 " (cutoff:3.500A) Processing helix chain '7' and resid 145 through 148 Processing helix chain '7' and resid 151 through 158 removed outlier: 3.657A pdb=" N LYS 7 157 " --> pdb=" O PRO 7 153 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL 7 158 " --> pdb=" O LEU 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 170 through 187 removed outlier: 3.625A pdb=" N GLU 7 174 " --> pdb=" O VAL 7 170 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL 7 183 " --> pdb=" O ASN 7 179 " (cutoff:3.500A) Processing helix chain '7' and resid 221 through 223 No H-bonds generated for 'chain '7' and resid 221 through 223' Processing helix chain 'H' and resid 43 through 49 removed outlier: 3.747A pdb=" N ALA H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS H 48 " --> pdb=" O PRO H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 67 removed outlier: 3.643A pdb=" N LEU H 56 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE H 63 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU H 65 " --> pdb=" O ALA H 61 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA H 67 " --> pdb=" O ILE H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 80 No H-bonds generated for 'chain 'H' and resid 78 through 80' Processing helix chain 'H' and resid 82 through 91 removed outlier: 3.711A pdb=" N ASP H 87 " --> pdb=" O ASP H 83 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG H 88 " --> pdb=" O ILE H 84 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN H 89 " --> pdb=" O MET H 85 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU H 91 " --> pdb=" O ASP H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 224 removed outlier: 3.593A pdb=" N LEU H 221 " --> pdb=" O GLN H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 230 Processing helix chain 'H' and resid 234 through 237 No H-bonds generated for 'chain 'H' and resid 234 through 237' Processing helix chain 'H' and resid 258 through 266 removed outlier: 3.592A pdb=" N ALA H 262 " --> pdb=" O LEU H 258 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 300 removed outlier: 3.655A pdb=" N MET H 290 " --> pdb=" O GLU H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 340 removed outlier: 3.917A pdb=" N THR H 332 " --> pdb=" O GLU H 328 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET H 333 " --> pdb=" O VAL H 329 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN H 339 " --> pdb=" O GLU H 335 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU H 340 " --> pdb=" O LEU H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 392 removed outlier: 4.221A pdb=" N ARG H 390 " --> pdb=" O ALA H 386 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE H 391 " --> pdb=" O ASN H 387 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS H 392 " --> pdb=" O ILE H 388 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 410 removed outlier: 3.786A pdb=" N SER H 408 " --> pdb=" O TRP H 404 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU H 410 " --> pdb=" O LEU H 406 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 419 No H-bonds generated for 'chain 'H' and resid 416 through 419' Processing helix chain 'H' and resid 421 through 433 removed outlier: 3.653A pdb=" N ILE H 431 " --> pdb=" O GLY H 427 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG H 432 " --> pdb=" O MET H 428 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 455 removed outlier: 3.740A pdb=" N LEU H 444 " --> pdb=" O GLU H 440 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 78 removed outlier: 3.626A pdb=" N LEU I 59 " --> pdb=" O CYS I 55 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS I 66 " --> pdb=" O MET I 62 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS I 68 " --> pdb=" O ARG I 64 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN I 78 " --> pdb=" O GLU I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 100 removed outlier: 3.506A pdb=" N LYS I 94 " --> pdb=" O GLU I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 171 removed outlier: 3.894A pdb=" N VAL I 170 " --> pdb=" O PRO I 166 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N MET I 171 " --> pdb=" O MET I 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 166 through 171' Processing helix chain 'I' and resid 188 through 190 No H-bonds generated for 'chain 'I' and resid 188 through 190' Processing helix chain 'I' and resid 194 through 197 No H-bonds generated for 'chain 'I' and resid 194 through 197' Processing helix chain 'I' and resid 200 through 203 No H-bonds generated for 'chain 'I' and resid 200 through 203' Processing helix chain 'I' and resid 205 through 210 Processing helix chain 'I' and resid 229 through 239 removed outlier: 4.125A pdb=" N ASN I 238 " --> pdb=" O LYS I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 273 removed outlier: 3.621A pdb=" N ARG I 265 " --> pdb=" O PRO I 261 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU I 273 " --> pdb=" O LYS I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 298 through 313 removed outlier: 3.952A pdb=" N LEU I 313 " --> pdb=" O LEU I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 357 through 366 removed outlier: 3.503A pdb=" N GLY I 363 " --> pdb=" O LYS I 359 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE I 364 " --> pdb=" O LYS I 360 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS I 365 " --> pdb=" O ILE I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 383 removed outlier: 3.986A pdb=" N VAL I 381 " --> pdb=" O LEU I 377 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR I 383 " --> pdb=" O THR I 379 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 396 removed outlier: 3.591A pdb=" N GLN I 393 " --> pdb=" O GLY I 389 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS I 396 " --> pdb=" O ILE I 392 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 406 Processing helix chain 'I' and resid 413 through 429 removed outlier: 3.509A pdb=" N LYS I 417 " --> pdb=" O ALA I 413 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU I 421 " --> pdb=" O LYS I 417 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG I 422 " --> pdb=" O GLN I 418 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN I 426 " --> pdb=" O ARG I 422 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS I 427 " --> pdb=" O VAL I 423 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL I 428 " --> pdb=" O MET I 424 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 90 removed outlier: 3.627A pdb=" N SER K 45 " --> pdb=" O SER K 41 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP K 46 " --> pdb=" O ASN K 42 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR K 48 " --> pdb=" O ASN K 44 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE K 49 " --> pdb=" O SER K 45 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS K 56 " --> pdb=" O LYS K 52 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU K 57 " --> pdb=" O LYS K 53 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU K 60 " --> pdb=" O LYS K 56 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU K 61 " --> pdb=" O GLU K 57 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU K 65 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP K 66 " --> pdb=" O THR K 62 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG K 73 " --> pdb=" O LYS K 69 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG K 77 " --> pdb=" O ARG K 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS K 80 " --> pdb=" O LYS K 76 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU K 85 " --> pdb=" O ARG K 81 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL K 86 " --> pdb=" O ALA K 82 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS K 87 " --> pdb=" O GLN K 83 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 187 removed outlier: 3.745A pdb=" N GLU K 186 " --> pdb=" O GLN K 182 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA K 187 " --> pdb=" O GLU K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 193 removed outlier: 3.678A pdb=" N VAL K 193 " --> pdb=" O GLU K 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 189 through 193' Processing helix chain 'K' and resid 196 through 201 removed outlier: 3.661A pdb=" N ILE K 201 " --> pdb=" O LEU K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 219 through 230 removed outlier: 4.122A pdb=" N SER K 229 " --> pdb=" O ALA K 225 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR K 230 " --> pdb=" O VAL K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 263 removed outlier: 3.904A pdb=" N VAL K 254 " --> pdb=" O GLY K 250 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG K 255 " --> pdb=" O PRO K 251 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP K 256 " --> pdb=" O ARG K 252 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE K 258 " --> pdb=" O VAL K 254 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG K 262 " --> pdb=" O PHE K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 305 removed outlier: 3.547A pdb=" N GLY K 305 " --> pdb=" O THR K 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 323 No H-bonds generated for 'chain 'K' and resid 321 through 323' Processing helix chain 'K' and resid 326 through 329 No H-bonds generated for 'chain 'K' and resid 326 through 329' Processing helix chain 'K' and resid 346 through 359 removed outlier: 3.860A pdb=" N LEU K 351 " --> pdb=" O ARG K 347 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE K 356 " --> pdb=" O ILE K 352 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS K 359 " --> pdb=" O THR K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 374 removed outlier: 3.550A pdb=" N ILE K 373 " --> pdb=" O SER K 370 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG K 374 " --> pdb=" O LEU K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 397 removed outlier: 3.929A pdb=" N ILE K 386 " --> pdb=" O VAL K 382 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET K 387 " --> pdb=" O ILE K 383 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN K 388 " --> pdb=" O ALA K 384 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG K 393 " --> pdb=" O GLU K 389 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL K 395 " --> pdb=" O GLY K 391 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 412 Processing helix chain 'L' and resid 58 through 98 removed outlier: 3.676A pdb=" N ARG L 62 " --> pdb=" O ASN L 58 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG L 68 " --> pdb=" O LEU L 64 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG L 69 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP L 72 " --> pdb=" O ARG L 68 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU L 74 " --> pdb=" O TYR L 70 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP L 83 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS L 86 " --> pdb=" O ARG L 82 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU L 87 " --> pdb=" O ASP L 83 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR L 91 " --> pdb=" O LEU L 87 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP L 94 " --> pdb=" O LYS L 90 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE L 95 " --> pdb=" O THR L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 169 No H-bonds generated for 'chain 'L' and resid 166 through 169' Processing helix chain 'L' and resid 187 through 202 removed outlier: 3.584A pdb=" N VAL L 196 " --> pdb=" O GLU L 192 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU L 199 " --> pdb=" O GLU L 195 " (cutoff:3.500A) Proline residue: L 200 - end of helix Processing helix chain 'L' and resid 205 through 210 removed outlier: 3.810A pdb=" N ARG L 209 " --> pdb=" O GLU L 205 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL L 210 " --> pdb=" O ILE L 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 205 through 210' Processing helix chain 'L' and resid 228 through 237 removed outlier: 3.615A pdb=" N ALA L 232 " --> pdb=" O LYS L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 272 removed outlier: 4.320A pdb=" N ILE L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE L 267 " --> pdb=" O ILE L 263 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA L 268 " --> pdb=" O ARG L 264 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS L 271 " --> pdb=" O PHE L 267 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 312 removed outlier: 3.607A pdb=" N GLN L 302 " --> pdb=" O ASP L 298 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU L 307 " --> pdb=" O ARG L 303 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU L 308 " --> pdb=" O THR L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 364 removed outlier: 3.844A pdb=" N ILE L 363 " --> pdb=" O GLU L 359 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS L 364 " --> pdb=" O ILE L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 376 through 383 removed outlier: 3.700A pdb=" N LYS L 381 " --> pdb=" O GLU L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 388 through 391 No H-bonds generated for 'chain 'L' and resid 388 through 391' Processing helix chain 'L' and resid 394 through 398 Processing helix chain 'L' and resid 401 through 405 removed outlier: 3.649A pdb=" N ASP L 405 " --> pdb=" O PHE L 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 401 through 405' Processing helix chain 'L' and resid 412 through 427 removed outlier: 3.774A pdb=" N MET L 416 " --> pdb=" O PRO L 412 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG L 420 " --> pdb=" O MET L 416 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU L 424 " --> pdb=" O ARG L 420 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 73 removed outlier: 3.627A pdb=" N ASP M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN M 39 " --> pdb=" O LYS M 35 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER M 46 " --> pdb=" O ARG M 42 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU M 48 " --> pdb=" O PHE M 44 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU M 51 " --> pdb=" O GLU M 47 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS M 53 " --> pdb=" O GLN M 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN M 56 " --> pdb=" O SER M 52 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL M 57 " --> pdb=" O HIS M 53 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU M 59 " --> pdb=" O ASN M 55 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU M 60 " --> pdb=" O ASN M 56 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS M 61 " --> pdb=" O VAL M 57 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE M 62 " --> pdb=" O MET M 58 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS M 68 " --> pdb=" O ASP M 64 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN M 71 " --> pdb=" O GLU M 67 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN M 72 " --> pdb=" O LYS M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 170 removed outlier: 3.654A pdb=" N ALA M 169 " --> pdb=" O SER M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 196 removed outlier: 3.702A pdb=" N GLU M 191 " --> pdb=" O ASP M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 202 No H-bonds generated for 'chain 'M' and resid 199 through 202' Processing helix chain 'M' and resid 206 through 210 Processing helix chain 'M' and resid 228 through 238 removed outlier: 3.553A pdb=" N ALA M 232 " --> pdb=" O LYS M 228 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG M 233 " --> pdb=" O THR M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 250 No H-bonds generated for 'chain 'M' and resid 248 through 250' Processing helix chain 'M' and resid 260 through 272 removed outlier: 3.576A pdb=" N ARG M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU M 269 " --> pdb=" O ASP M 265 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA M 270 " --> pdb=" O ALA M 266 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU M 272 " --> pdb=" O ALA M 268 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 311 removed outlier: 4.159A pdb=" N ARG M 303 " --> pdb=" O ARG M 299 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR M 304 " --> pdb=" O GLU M 300 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET M 305 " --> pdb=" O VAL M 301 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU M 308 " --> pdb=" O THR M 304 " (cutoff:3.500A) Processing helix chain 'M' and resid 354 through 365 Processing helix chain 'M' and resid 376 through 382 Processing helix chain 'M' and resid 388 through 405 removed outlier: 3.512A pdb=" N ALA M 393 " --> pdb=" O ALA M 389 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU M 397 " --> pdb=" O ALA M 393 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY M 399 " --> pdb=" O THR M 395 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE M 401 " --> pdb=" O GLU M 397 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN M 405 " --> pdb=" O ILE M 401 " (cutoff:3.500A) Processing helix chain 'M' and resid 414 through 417 No H-bonds generated for 'chain 'M' and resid 414 through 417' Processing helix chain 'J' and resid 15 through 18 No H-bonds generated for 'chain 'J' and resid 15 through 18' Processing helix chain 'J' and resid 20 through 64 removed outlier: 4.210A pdb=" N LYS J 26 " --> pdb=" O TYR J 22 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE J 27 " --> pdb=" O PHE J 23 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR J 30 " --> pdb=" O LYS J 26 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS J 33 " --> pdb=" O GLU J 29 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR J 38 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU J 39 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN J 47 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG J 48 " --> pdb=" O LEU J 44 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS J 59 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP J 60 " --> pdb=" O ARG J 56 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 140 Processing helix chain 'J' and resid 154 through 163 removed outlier: 3.870A pdb=" N LYS J 158 " --> pdb=" O THR J 154 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU J 159 " --> pdb=" O LYS J 155 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE J 160 " --> pdb=" O GLN J 156 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS J 161 " --> pdb=" O ILE J 157 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL J 163 " --> pdb=" O GLU J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 169 No H-bonds generated for 'chain 'J' and resid 166 through 169' Processing helix chain 'J' and resid 171 through 177 removed outlier: 3.573A pdb=" N LEU J 177 " --> pdb=" O LEU J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 205 removed outlier: 4.178A pdb=" N ALA J 199 " --> pdb=" O LYS J 195 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA J 201 " --> pdb=" O LEU J 197 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS J 205 " --> pdb=" O ALA J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 231 through 239 removed outlier: 3.613A pdb=" N GLU J 239 " --> pdb=" O VAL J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 276 removed outlier: 3.539A pdb=" N GLN J 269 " --> pdb=" O ASP J 265 " (cutoff:3.500A) Processing helix chain 'J' and resid 323 through 333 removed outlier: 3.802A pdb=" N ILE J 327 " --> pdb=" O ALA J 323 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE J 330 " --> pdb=" O GLU J 326 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS J 331 " --> pdb=" O ILE J 327 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG J 333 " --> pdb=" O ARG J 329 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 349 removed outlier: 3.623A pdb=" N ALA J 347 " --> pdb=" O LEU J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 357 through 372 removed outlier: 4.267A pdb=" N CYS J 362 " --> pdb=" O VAL J 358 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY J 366 " --> pdb=" O CYS J 362 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET J 367 " --> pdb=" O THR J 363 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU J 370 " --> pdb=" O GLY J 366 " (cutoff:3.500A) Processing helix chain 'J' and resid 381 through 396 removed outlier: 3.518A pdb=" N GLY J 387 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU J 395 " --> pdb=" O ASN J 391 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'a' and resid 159 through 162 Processing sheet with id= B, first strand: chain 'a' and resid 63 through 65 removed outlier: 3.563A pdb=" N GLY a 71 " --> pdb=" O VAL a 135 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE a 131 " --> pdb=" O ASN a 75 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS a 147 " --> pdb=" O VAL a 155 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL a 155 " --> pdb=" O LYS a 147 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'b' and resid 161 through 164 Processing sheet with id= D, first strand: chain 'b' and resid 156 through 158 removed outlier: 6.377A pdb=" N ALA b 73 " --> pdb=" O LEU b 66 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU b 66 " --> pdb=" O ALA b 73 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N TYR b 75 " --> pdb=" O VAL b 64 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL b 64 " --> pdb=" O TYR b 75 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'c' and resid 161 through 164 removed outlier: 3.545A pdb=" N ALA c 46 " --> pdb=" O ILE c 35 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'c' and resid 156 through 158 removed outlier: 3.521A pdb=" N SER c 150 " --> pdb=" O PHE c 134 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE c 134 " --> pdb=" O SER c 150 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN c 69 " --> pdb=" O ILE c 72 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL c 74 " --> pdb=" O LYS c 67 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LYS c 67 " --> pdb=" O VAL c 74 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL c 76 " --> pdb=" O LEU c 65 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU c 65 " --> pdb=" O VAL c 76 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'd' and resid 159 through 162 removed outlier: 3.772A pdb=" N ASP d 218 " --> pdb=" O LYS d 214 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'd' and resid 62 through 64 removed outlier: 3.796A pdb=" N GLY d 135 " --> pdb=" O LYS d 144 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS d 144 " --> pdb=" O GLY d 135 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'e' and resid 161 through 164 removed outlier: 3.625A pdb=" N GLN e 210 " --> pdb=" O VAL e 42 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS e 221 " --> pdb=" O CYS e 213 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR e 215 " --> pdb=" O GLY e 219 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'e' and resid 145 through 150 removed outlier: 3.585A pdb=" N GLY e 138 " --> pdb=" O GLN e 146 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N CYS e 68 " --> pdb=" O GLU e 61 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLU e 61 " --> pdb=" O CYS e 68 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET e 70 " --> pdb=" O ILE e 59 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE e 59 " --> pdb=" O MET e 70 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'f' and resid 157 through 160 removed outlier: 3.524A pdb=" N LEU f 37 " --> pdb=" O VAL f 44 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE f 212 " --> pdb=" O TYR f 224 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR f 222 " --> pdb=" O ILE f 214 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'f' and resid 62 through 64 removed outlier: 3.914A pdb=" N GLY f 140 " --> pdb=" O ASP f 137 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'g' and resid 158 through 161 Processing sheet with id= N, first strand: chain 'g' and resid 63 through 66 removed outlier: 3.899A pdb=" N MET g 146 " --> pdb=" O TRP g 154 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP g 154 " --> pdb=" O MET g 146 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER g 152 " --> pdb=" O GLU g 148 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'h' and resid 124 through 128 removed outlier: 3.531A pdb=" N ILE h 173 " --> pdb=" O PHE h 188 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'h' and resid 34 through 36 removed outlier: 4.189A pdb=" N VAL h 110 " --> pdb=" O LEU h 122 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'h' and resid 20 through 22 removed outlier: 3.550A pdb=" N ASN h 28 " --> pdb=" O THR h 20 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR h 22 " --> pdb=" O ILE h 26 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE h 26 " --> pdb=" O THR h 22 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'i' and resid 124 through 127 removed outlier: 3.802A pdb=" N PHE i 8 " --> pdb=" O GLY i 11 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'i' and resid 118 through 121 removed outlier: 3.684A pdb=" N SER i 118 " --> pdb=" O HIS i 114 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY i 102 " --> pdb=" O HIS i 109 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL i 100 " --> pdb=" O PHE i 111 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS i 43 " --> pdb=" O ARG i 36 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG i 36 " --> pdb=" O CYS i 43 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLY i 45 " --> pdb=" O LEU i 34 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU i 34 " --> pdb=" O GLY i 45 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'j' and resid 135 through 139 removed outlier: 5.681A pdb=" N ILE j 10 " --> pdb=" O ASP j 25 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP j 25 " --> pdb=" O ILE j 10 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS j 19 " --> pdb=" O GLY j 16 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA j 184 " --> pdb=" O LEU j 199 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'j' and resid 42 through 45 Processing sheet with id= V, first strand: chain 'j' and resid 28 through 30 removed outlier: 3.605A pdb=" N LEU j 28 " --> pdb=" O SER j 36 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SER j 30 " --> pdb=" O GLY j 34 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLY j 34 " --> pdb=" O SER j 30 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'k' and resid 130 through 132 removed outlier: 3.601A pdb=" N SER k 12 " --> pdb=" O VAL k 9 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'k' and resid 124 through 127 removed outlier: 3.729A pdb=" N THR k 124 " --> pdb=" O ASP k 120 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N MET k 44 " --> pdb=" O GLN k 37 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLN k 37 " --> pdb=" O MET k 44 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE k 46 " --> pdb=" O THR k 35 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N THR k 35 " --> pdb=" O PHE k 46 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'l' and resid 126 through 130 Processing sheet with id= Z, first strand: chain 'l' and resid 98 through 105 removed outlier: 3.662A pdb=" N THR l 99 " --> pdb=" O VAL l 115 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR l 105 " --> pdb=" O GLY l 109 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE l 112 " --> pdb=" O GLY l 124 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY l 124 " --> pdb=" O ILE l 112 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'l' and resid 178 through 180 Processing sheet with id= AB, first strand: chain 'l' and resid 34 through 38 removed outlier: 6.127A pdb=" N LEU l 41 " --> pdb=" O ILE l 37 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'm' and resid 136 through 140 removed outlier: 5.043A pdb=" N THR m 11 " --> pdb=" O ASP m 26 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE m 204 " --> pdb=" O GLU m 215 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'm' and resid 50 through 56 removed outlier: 4.063A pdb=" N VAL m 122 " --> pdb=" O GLU m 134 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP m 126 " --> pdb=" O SER m 130 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N SER m 130 " --> pdb=" O ASP m 126 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'm' and resid 29 through 31 removed outlier: 3.878A pdb=" N ASN m 29 " --> pdb=" O SER m 37 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER m 37 " --> pdb=" O ASN m 29 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR m 31 " --> pdb=" O ILE m 35 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE m 35 " --> pdb=" O THR m 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'n' and resid 141 through 143 removed outlier: 3.713A pdb=" N LEU n 142 " --> pdb=" O SER n 13 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'n' and resid 42 through 44 Processing sheet with id= AH, first strand: chain 'A' and resid 159 through 162 removed outlier: 3.562A pdb=" N THR A 162 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS A 223 " --> pdb=" O THR A 220 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A' and resid 63 through 65 removed outlier: 3.728A pdb=" N LYS A 147 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 155 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.695A pdb=" N ALA B 46 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 43 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 213 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 236 " --> pdb=" O ILE B 213 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'B' and resid 72 through 77 removed outlier: 3.617A pdb=" N VAL B 74 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.608A pdb=" N ILE C 37 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 44 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 156 through 158 removed outlier: 3.559A pdb=" N ASN C 69 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL C 74 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LYS C 67 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL C 76 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'D' and resid 159 through 162 removed outlier: 3.925A pdb=" N ASP D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'D' and resid 62 through 64 removed outlier: 3.590A pdb=" N THR D 131 " --> pdb=" O THR D 148 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY D 135 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS D 144 " --> pdb=" O GLY D 135 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'E' and resid 161 through 164 Processing sheet with id= AQ, first strand: chain 'E' and resid 156 through 158 removed outlier: 3.551A pdb=" N ASP E 140 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY E 138 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU E 134 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 66 " --> pdb=" O ASP E 63 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N CYS E 68 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU E 61 " --> pdb=" O CYS E 68 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N MET E 70 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE E 59 " --> pdb=" O MET E 70 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'F' and resid 157 through 160 removed outlier: 3.539A pdb=" N VAL F 46 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE F 212 " --> pdb=" O TYR F 224 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR F 222 " --> pdb=" O ILE F 214 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'F' and resid 73 through 75 removed outlier: 3.758A pdb=" N LEU F 131 " --> pdb=" O PHE F 146 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY F 140 " --> pdb=" O ASP F 137 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR F 153 " --> pdb=" O GLU F 145 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'F' and resid 62 through 66 removed outlier: 6.666A pdb=" N MET F 69 " --> pdb=" O CYS F 65 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'G' and resid 158 through 161 removed outlier: 3.638A pdb=" N GLU G 211 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'G' and resid 64 through 66 removed outlier: 3.501A pdb=" N TYR G 145 " --> pdb=" O PHE G 134 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET G 146 " --> pdb=" O TRP G 154 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP G 154 " --> pdb=" O MET G 146 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain '1' and resid 124 through 127 removed outlier: 3.567A pdb=" N ARG 1 174 " --> pdb=" O ALA 1 16 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain '1' and resid 34 through 36 removed outlier: 3.515A pdb=" N ASP 1 103 " --> pdb=" O LYS 1 107 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain '1' and resid 20 through 22 removed outlier: 3.850A pdb=" N ASN 1 28 " --> pdb=" O THR 1 20 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR 1 22 " --> pdb=" O ILE 1 26 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE 1 26 " --> pdb=" O THR 1 22 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain '2' and resid 124 through 128 removed outlier: 5.808A pdb=" N THR 2 2 " --> pdb=" O ASP 2 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP 2 17 " --> pdb=" O THR 2 2 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL 2 175 " --> pdb=" O LEU 2 187 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain '2' and resid 119 through 121 removed outlier: 3.708A pdb=" N GLY 2 102 " --> pdb=" O HIS 2 109 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR 2 97 " --> pdb=" O ALA 2 46 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE 2 41 " --> pdb=" O SER 2 38 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS 2 43 " --> pdb=" O ARG 2 36 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARG 2 36 " --> pdb=" O CYS 2 43 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLY 2 45 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU 2 34 " --> pdb=" O GLY 2 45 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain '3' and resid 135 through 139 removed outlier: 5.506A pdb=" N ILE 3 10 " --> pdb=" O ASP 3 25 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP 3 25 " --> pdb=" O ILE 3 10 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain '3' and resid 42 through 45 removed outlier: 3.705A pdb=" N THR 3 53 " --> pdb=" O GLY 3 105 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY 3 105 " --> pdb=" O THR 3 53 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN 3 112 " --> pdb=" O LYS 3 117 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS 3 117 " --> pdb=" O ASN 3 112 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain '3' and resid 28 through 30 removed outlier: 6.703A pdb=" N SER 3 30 " --> pdb=" O GLY 3 34 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY 3 34 " --> pdb=" O SER 3 30 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain '4' and resid 130 through 132 removed outlier: 3.706A pdb=" N SER 4 12 " --> pdb=" O VAL 4 9 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL 4 181 " --> pdb=" O VAL 4 192 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL 4 192 " --> pdb=" O VAL 4 181 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain '4' and resid 124 through 127 removed outlier: 3.831A pdb=" N THR 4 124 " --> pdb=" O ASP 4 120 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS 4 113 " --> pdb=" O ASP 4 108 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP 4 108 " --> pdb=" O LYS 4 113 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR 4 42 " --> pdb=" O SER 4 39 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET 4 44 " --> pdb=" O GLN 4 37 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLN 4 37 " --> pdb=" O MET 4 44 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE 4 46 " --> pdb=" O THR 4 35 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N THR 4 35 " --> pdb=" O PHE 4 46 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain '5' and resid 126 through 129 removed outlier: 3.629A pdb=" N LEU 5 177 " --> pdb=" O GLY 5 189 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY 5 189 " --> pdb=" O LEU 5 177 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N HIS 5 179 " --> pdb=" O TYR 5 187 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR 5 187 " --> pdb=" O HIS 5 179 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR 5 181 " --> pdb=" O TRP 5 185 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N TRP 5 185 " --> pdb=" O THR 5 181 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain '5' and resid 98 through 105 removed outlier: 3.546A pdb=" N GLY 5 103 " --> pdb=" O THR 5 111 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR 5 105 " --> pdb=" O GLY 5 109 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE 5 112 " --> pdb=" O GLY 5 124 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY 5 124 " --> pdb=" O ILE 5 112 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain '5' and resid 34 through 38 removed outlier: 3.535A pdb=" N ILE 5 37 " --> pdb=" O LEU 5 41 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU 5 41 " --> pdb=" O ILE 5 37 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain '6' and resid 136 through 140 removed outlier: 5.235A pdb=" N THR 6 11 " --> pdb=" O ASP 6 26 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain '6' and resid 50 through 56 removed outlier: 3.738A pdb=" N THR 6 109 " --> pdb=" O PHE 6 125 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain '6' and resid 29 through 31 removed outlier: 3.621A pdb=" N ASN 6 29 " --> pdb=" O SER 6 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER 6 37 " --> pdb=" O ASN 6 29 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR 6 31 " --> pdb=" O ILE 6 35 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE 6 35 " --> pdb=" O THR 6 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= BL Processing sheet with id= BM, first strand: chain '7' and resid 141 through 144 removed outlier: 3.850A pdb=" N VAL 7 11 " --> pdb=" O THR 7 144 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain '7' and resid 42 through 44 Processing sheet with id= BO, first strand: chain '7' and resid 27 through 30 removed outlier: 6.629A pdb=" N TYR 7 30 " --> pdb=" O LEU 7 34 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU 7 34 " --> pdb=" O TYR 7 30 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'H' and resid 97 through 99 removed outlier: 3.623A pdb=" N LEU H 185 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP H 177 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE H 183 " --> pdb=" O ASP H 177 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'H' and resid 154 through 157 removed outlier: 5.590A pdb=" N ASN H 148 " --> pdb=" O CYS H 102 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N CYS H 102 " --> pdb=" O ASN H 148 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'H' and resid 245 through 249 removed outlier: 8.494A pdb=" N ILE H 246 " --> pdb=" O ILE H 349 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL H 351 " --> pdb=" O ILE H 246 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU H 248 " --> pdb=" O VAL H 351 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE H 353 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS H 304 " --> pdb=" O LYS H 350 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N MET H 352 " --> pdb=" O CYS H 304 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE H 306 " --> pdb=" O MET H 352 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ALA H 354 " --> pdb=" O ILE H 306 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE H 308 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR H 270 " --> pdb=" O ILE H 305 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N PHE H 307 " --> pdb=" O THR H 270 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE H 272 " --> pdb=" O PHE H 307 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASP H 309 " --> pdb=" O ILE H 272 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL H 274 " --> pdb=" O ASP H 309 " (cutoff:3.500A) No H-bonds generated for sheet with id= BR Processing sheet with id= BS, first strand: chain 'I' and resid 146 through 150 removed outlier: 3.503A pdb=" N THR I 108 " --> pdb=" O THR I 121 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE I 119 " --> pdb=" O GLU I 110 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ILE I 112 " --> pdb=" O HIS I 117 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N HIS I 117 " --> pdb=" O ILE I 112 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'I' and resid 348 through 350 removed outlier: 3.863A pdb=" N TYR I 222 " --> pdb=" O ILE I 348 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL I 219 " --> pdb=" O VAL I 324 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET I 326 " --> pdb=" O VAL I 219 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR I 243 " --> pdb=" O ILE I 278 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N PHE I 280 " --> pdb=" O THR I 243 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU I 245 " --> pdb=" O PHE I 280 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP I 282 " --> pdb=" O LEU I 245 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE I 247 " --> pdb=" O ASP I 282 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'K' and resid 135 through 139 removed outlier: 3.644A pdb=" N MET K 135 " --> pdb=" O PHE K 99 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL K 137 " --> pdb=" O GLY K 97 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY K 97 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE K 109 " --> pdb=" O LEU K 100 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N THR K 107 " --> pdb=" O PRO K 102 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'K' and resid 315 through 318 removed outlier: 6.347A pdb=" N VAL K 209 " --> pdb=" O MET K 316 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N THR K 318 " --> pdb=" O VAL K 209 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU K 211 " --> pdb=" O THR K 318 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU K 210 " --> pdb=" O ASP K 335 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS K 337 " --> pdb=" O LEU K 210 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR K 212 " --> pdb=" O LYS K 337 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU K 339 " --> pdb=" O TYR K 212 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'K' and resid 233 through 237 Processing sheet with id= BX, first strand: chain 'L' and resid 145 through 147 removed outlier: 3.718A pdb=" N GLU L 107 " --> pdb=" O LYS L 120 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE L 118 " --> pdb=" O MET L 109 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'L' and resid 345 through 348 removed outlier: 3.553A pdb=" N LEU L 219 " --> pdb=" O ARG L 345 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR L 221 " --> pdb=" O VAL L 347 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N CYS L 276 " --> pdb=" O LYS L 322 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE L 324 " --> pdb=" O CYS L 276 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE L 278 " --> pdb=" O ILE L 324 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA L 326 " --> pdb=" O ILE L 278 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET L 280 " --> pdb=" O ALA L 326 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN L 242 " --> pdb=" O ILE L 277 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE L 279 " --> pdb=" O ASN L 242 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE L 244 " --> pdb=" O PHE L 279 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ASP L 281 " --> pdb=" O ILE L 244 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER L 246 " --> pdb=" O ASP L 281 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'M' and resid 126 through 130 removed outlier: 3.535A pdb=" N GLU M 84 " --> pdb=" O VAL M 118 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS M 120 " --> pdb=" O VAL M 82 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL M 82 " --> pdb=" O LYS M 120 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP M 157 " --> pdb=" O GLY M 147 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'M' and resid 345 through 348 removed outlier: 3.678A pdb=" N TYR M 221 " --> pdb=" O ILE M 347 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR M 276 " --> pdb=" O LYS M 322 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU M 324 " --> pdb=" O THR M 276 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE M 278 " --> pdb=" O LEU M 324 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA M 326 " --> pdb=" O ILE M 278 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE M 280 " --> pdb=" O ALA M 326 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE M 279 " --> pdb=" O LEU M 244 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'J' and resid 112 through 115 removed outlier: 3.619A pdb=" N LEU J 115 " --> pdb=" O TYR J 71 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU J 85 " --> pdb=" O ILE J 76 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE J 78 " --> pdb=" O LYS J 83 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LYS J 83 " --> pdb=" O ILE J 78 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'J' and resid 209 through 213 removed outlier: 3.826A pdb=" N VAL J 213 " --> pdb=" O PHE J 246 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP J 248 " --> pdb=" O VAL J 213 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL J 185 " --> pdb=" O MET J 292 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP J 311 " --> pdb=" O GLY J 184 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE J 186 " --> pdb=" O ASP J 311 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS J 313 " --> pdb=" O ILE J 186 " (cutoff:3.500A) 2584 hydrogen bonds defined for protein. 7437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 28.70 Time building geometry restraints manager: 21.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.19: 114 1.19 - 1.38: 24312 1.38 - 1.58: 42816 1.58 - 1.77: 1411 1.77 - 1.96: 391 Bond restraints: 69044 Sorted by residual: bond pdb=" CA LEU b 67 " pdb=" C LEU b 67 " ideal model delta sigma weight residual 1.526 1.413 0.113 9.20e-03 1.18e+04 1.52e+02 bond pdb=" C VAL g 137 " pdb=" N ASP g 138 " ideal model delta sigma weight residual 1.328 1.429 -0.101 8.50e-03 1.38e+04 1.40e+02 bond pdb=" C ASN G 244 " pdb=" O ASN G 244 " ideal model delta sigma weight residual 1.231 0.999 0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C ILE f 233 " pdb=" OXT ILE f 233 " ideal model delta sigma weight residual 1.231 0.999 0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C GLN a 242 " pdb=" O GLN a 242 " ideal model delta sigma weight residual 1.231 1.000 0.231 2.00e-02 2.50e+03 1.34e+02 ... (remaining 69039 not shown) Histogram of bond angle deviations from ideal: 88.11 - 98.91: 97 98.91 - 109.70: 15152 109.70 - 120.50: 52883 120.50 - 131.29: 25016 131.29 - 142.09: 170 Bond angle restraints: 93318 Sorted by residual: angle pdb=" PB ATP M 501 " pdb=" O3B ATP M 501 " pdb=" PG ATP M 501 " ideal model delta sigma weight residual 139.87 126.03 13.84 1.00e+00 1.00e+00 1.92e+02 angle pdb=" N1 ATP H 502 " pdb=" C2 ATP H 502 " pdb=" N3 ATP H 502 " ideal model delta sigma weight residual 128.69 115.02 13.67 1.00e+00 1.00e+00 1.87e+02 angle pdb=" N1 ATP K 501 " pdb=" C2 ATP K 501 " pdb=" N3 ATP K 501 " ideal model delta sigma weight residual 128.69 116.32 12.37 1.00e+00 1.00e+00 1.53e+02 angle pdb=" CA ASP l 125 " pdb=" CB ASP l 125 " pdb=" CG ASP l 125 " ideal model delta sigma weight residual 112.60 100.82 11.78 1.00e+00 1.00e+00 1.39e+02 angle pdb=" N1 ATP M 501 " pdb=" C2 ATP M 501 " pdb=" N3 ATP M 501 " ideal model delta sigma weight residual 128.69 117.09 11.60 1.00e+00 1.00e+00 1.35e+02 ... (remaining 93313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.68: 40265 27.68 - 55.35: 1129 55.35 - 83.03: 379 83.03 - 110.70: 53 110.70 - 138.38: 1 Dihedral angle restraints: 41827 sinusoidal: 16832 harmonic: 24995 Sorted by residual: dihedral pdb=" CA ARG E 128 " pdb=" C ARG E 128 " pdb=" N PRO E 129 " pdb=" CA PRO E 129 " ideal model delta harmonic sigma weight residual -180.00 -119.17 -60.83 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA ILE I 339 " pdb=" C ILE I 339 " pdb=" N ARG I 340 " pdb=" CA ARG I 340 " ideal model delta harmonic sigma weight residual 180.00 124.10 55.90 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ARG H 367 " pdb=" C ARG H 367 " pdb=" N PRO H 368 " pdb=" CA PRO H 368 " ideal model delta harmonic sigma weight residual 180.00 -129.88 -50.12 0 5.00e+00 4.00e-02 1.00e+02 ... (remaining 41824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.203: 9416 0.203 - 0.405: 1041 0.405 - 0.608: 77 0.608 - 0.811: 4 0.811 - 1.013: 1 Chirality restraints: 10539 Sorted by residual: chirality pdb=" CA LEU K 51 " pdb=" N LEU K 51 " pdb=" C LEU K 51 " pdb=" CB LEU K 51 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.57e+01 chirality pdb=" CA GLN c 95 " pdb=" N GLN c 95 " pdb=" C GLN c 95 " pdb=" CB GLN c 95 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CA GLU e 123 " pdb=" N GLU e 123 " pdb=" C GLU e 123 " pdb=" CB GLU e 123 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 ... (remaining 10536 not shown) Planarity restraints: 12050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 2 " 0.197 2.00e-02 2.50e+03 1.28e-01 3.27e+02 pdb=" CG TYR D 2 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR D 2 " -0.127 2.00e-02 2.50e+03 pdb=" CD2 TYR D 2 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR D 2 " -0.070 2.00e-02 2.50e+03 pdb=" CE2 TYR D 2 " -0.154 2.00e-02 2.50e+03 pdb=" CZ TYR D 2 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 2 " 0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 153 " 0.207 2.00e-02 2.50e+03 1.17e-01 2.72e+02 pdb=" CG TYR A 153 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR A 153 " -0.114 2.00e-02 2.50e+03 pdb=" CD2 TYR A 153 " -0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR A 153 " -0.060 2.00e-02 2.50e+03 pdb=" CE2 TYR A 153 " -0.120 2.00e-02 2.50e+03 pdb=" CZ TYR A 153 " 0.049 2.00e-02 2.50e+03 pdb=" OH TYR A 153 " 0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 136 " 0.198 2.00e-02 2.50e+03 1.14e-01 2.60e+02 pdb=" CG TYR F 136 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR F 136 " -0.066 2.00e-02 2.50e+03 pdb=" CD2 TYR F 136 " -0.095 2.00e-02 2.50e+03 pdb=" CE1 TYR F 136 " -0.100 2.00e-02 2.50e+03 pdb=" CE2 TYR F 136 " -0.077 2.00e-02 2.50e+03 pdb=" CZ TYR F 136 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 136 " 0.183 2.00e-02 2.50e+03 ... (remaining 12047 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 17 2.06 - 2.77: 9997 2.77 - 3.48: 90795 3.48 - 4.19: 158060 4.19 - 4.90: 273344 Nonbonded interactions: 532213 Sorted by model distance: nonbonded pdb=" NH1 ARG b 4 " pdb=" OE1 GLU e 117 " model vdw 1.354 2.520 nonbonded pdb=" CZ ARG b 4 " pdb=" OE2 GLU e 117 " model vdw 1.432 3.270 nonbonded pdb=" OD1 ASN H 467 " pdb=" OXT ASN H 467 " model vdw 1.454 3.040 nonbonded pdb=" NH1 ARG b 4 " pdb=" CD GLU e 117 " model vdw 1.550 3.350 nonbonded pdb=" NH1 ARG b 4 " pdb=" OE2 GLU e 117 " model vdw 1.610 2.520 ... (remaining 532208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain 'h' } ncs_group { reference = chain '2' selection = chain 'i' } ncs_group { reference = chain '3' selection = chain 'j' } ncs_group { reference = chain '4' selection = chain 'k' } ncs_group { reference = chain '5' selection = chain 'l' } ncs_group { reference = chain '6' selection = chain 'm' } ncs_group { reference = chain '7' selection = (chain 'n' and resid 1 through 229) } ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = (chain 'F' and resid 3 through 233) selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 6 5.21 5 S 245 5.16 5 C 42802 2.51 5 N 11637 2.21 5 O 13176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 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: 0.050 Extract box with map and model: 16.670 Check model and map are aligned: 0.780 Process input model: 132.470 Find NCS groups from input model: 4.680 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Set scattering table: 0.500 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 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 : 0.026 0.232 69044 Z= 1.729 Angle : 2.510 25.174 93318 Z= 1.636 Chirality : 0.126 1.013 10539 Planarity : 0.019 0.259 12050 Dihedral : 15.513 138.380 25821 Min Nonbonded Distance : 1.354 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 1.77 % Allowed : 7.67 % Favored : 90.56 % Rotamer Outliers : 1.95 % Cbeta Deviations : 1.25 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -4.17 (0.07), residues: 8602 helix: -3.49 (0.06), residues: 3082 sheet: -1.44 (0.12), residues: 1731 loop : -2.65 (0.08), residues: 3789 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5161 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 5018 time to evaluate : 6.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 143 outliers final: 40 residues processed: 5065 average time/residue: 0.7225 time to fit residues: 6093.5911 Evaluate side-chains 3638 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 3598 time to evaluate : 5.919 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 40 outliers final: 2 residues processed: 40 average time/residue: 0.5681 time to fit residues: 49.4188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 722 optimal weight: 6.9990 chunk 648 optimal weight: 0.8980 chunk 360 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 437 optimal weight: 0.9980 chunk 346 optimal weight: 4.9990 chunk 670 optimal weight: 7.9990 chunk 259 optimal weight: 1.9990 chunk 407 optimal weight: 7.9990 chunk 499 optimal weight: 3.9990 chunk 777 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 121 GLN a 172 ASN ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 244 ASN c 151 ASN ** c 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 106 GLN f 4 ASN f 20 GLN ** f 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 151 ASN g 29 ASN g 64 GLN ** g 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 117 GLN g 191 GLN g 244 ASN h 145 ASN ** h 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 30 ASN i 66 HIS i 144 GLN i 165 ASN ** i 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 200 GLN j 31 GLN j 47 HIS j 156 ASN ** j 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 37 GLN k 101 ASN ** k 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 66 HIS ** l 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 176 ASN l 191 HIS ** m 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 197 GLN n 26 ASN n 78 ASN n 102 GLN n 108 ASN ** n 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 GLN A 30 ASN ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN A 175 ASN C 20 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS D 160 GLN ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN G 29 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 HIS 1 38 HIS 1 69 GLN 2 85 GLN ** 2 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 71 ASN ** 4 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 65 GLN 4 101 ASN ** 4 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 166 GLN 5 208 ASN 6 36 ASN ** 6 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 18 ASN 7 37 ASN 7 61 GLN 7 74 ASN 7 78 ASN 7 211 ASN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 339 GLN I 238 ASN I 295 ASN I 352 ASN ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 HIS K 83 GLN K 244 HIS L 93 ASN L 317 ASN ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 143 ASN ** M 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 69044 Z= 0.273 Angle : 0.777 17.180 93318 Z= 0.414 Chirality : 0.048 0.295 10539 Planarity : 0.006 0.091 12050 Dihedral : 6.655 87.755 9480 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.89 % Favored : 95.80 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.04 % 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: -2.09 (0.08), residues: 8602 helix: -1.31 (0.08), residues: 3171 sheet: -0.66 (0.12), residues: 1764 loop : -1.70 (0.09), residues: 3667 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4256 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 4237 time to evaluate : 6.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 4 residues processed: 4242 average time/residue: 0.6709 time to fit residues: 4744.4753 Evaluate side-chains 3415 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 3411 time to evaluate : 5.859 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.5119 time to fit residues: 11.9575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 432 optimal weight: 4.9990 chunk 241 optimal weight: 0.8980 chunk 646 optimal weight: 0.4980 chunk 529 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 778 optimal weight: 9.9990 chunk 841 optimal weight: 9.9990 chunk 693 optimal weight: 0.0980 chunk 772 optimal weight: 7.9990 chunk 265 optimal weight: 3.9990 chunk 624 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 218 ASN c 20 GLN ** c 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 30 GLN ** f 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 GLN ** g 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 178 HIS g 203 ASN h 38 HIS h 69 GLN h 157 HIS h 161 GLN h 195 GLN i 30 ASN ** i 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 165 ASN ** i 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 112 ASN j 168 GLN j 172 ASN ** k 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 176 ASN l 179 HIS m 95 HIS m 159 GLN m 197 GLN n 26 ASN n 78 ASN n 149 HIS n 194 ASN A 28 GLN ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN C 30 HIS ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN E 106 GLN E 225 ASN F 92 ASN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS G 114 GLN G 143 HIS 1 53 GLN 1 69 GLN 1 141 ASN 1 161 GLN ** 2 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 114 HIS ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 63 ASN ** 4 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 166 GLN 6 8 ASN 6 36 ASN ** 6 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 92 ASN ** 6 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 26 ASN 7 37 ASN 7 61 GLN 7 74 ASN 7 120 GLN 7 152 ASN 7 171 GLN H 89 GLN I 239 GLN ** I 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 HIS ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 302 GLN ** J 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 379 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.109 69044 Z= 0.214 Angle : 0.689 15.897 93318 Z= 0.362 Chirality : 0.046 0.247 10539 Planarity : 0.005 0.080 12050 Dihedral : 5.982 82.480 9480 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.73 % Favored : 96.01 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.08), residues: 8602 helix: -0.22 (0.09), residues: 3169 sheet: -0.27 (0.12), residues: 1734 loop : -1.30 (0.09), residues: 3699 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4096 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 4088 time to evaluate : 5.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 4090 average time/residue: 0.7012 time to fit residues: 4821.3886 Evaluate side-chains 3343 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3343 time to evaluate : 5.990 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.2923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 769 optimal weight: 8.9990 chunk 585 optimal weight: 10.0000 chunk 404 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 371 optimal weight: 0.5980 chunk 522 optimal weight: 5.9990 chunk 781 optimal weight: 5.9990 chunk 827 optimal weight: 6.9990 chunk 408 optimal weight: 0.1980 chunk 740 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 241 GLN c 58 GLN c 88 ASN ** c 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 53 GLN ** d 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 118 ASN f 165 GLN ** g 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 195 GLN i 85 GLN i 144 GLN i 165 ASN ** i 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 37 GLN ** k 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 ASN ** k 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 89 GLN l 176 ASN l 191 HIS m 76 HIS m 135 GLN ** m 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 197 GLN ** n 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 149 HIS ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN B 241 GLN C 20 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN E 149 HIS E 225 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 HIS G 29 ASN ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 HIS G 114 GLN ** 2 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 114 HIS 3 37 ASN ** 3 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 63 ASN ** 4 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 8 ASN ** 6 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 61 GLN 7 74 ASN I 150 HIS I 239 GLN ** I 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 69044 Z= 0.263 Angle : 0.685 13.236 93318 Z= 0.360 Chirality : 0.045 0.247 10539 Planarity : 0.005 0.080 12050 Dihedral : 5.783 81.433 9480 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.58 % Favored : 96.20 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.09), residues: 8602 helix: 0.14 (0.09), residues: 3174 sheet: -0.17 (0.12), residues: 1773 loop : -1.06 (0.10), residues: 3655 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3897 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 3887 time to evaluate : 5.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 3889 average time/residue: 0.6627 time to fit resiTraceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 295, in __init__ self.caller(self.set_rotamer_restraints) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 318, in caller self.log.flush() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/libtbx/utils.py", line 1570, in flush if (flush is not None): flush() IOError: [Errno 28] No space left on device