Starting phenix.real_space_refine (version: dev) on Fri Apr 8 07:23:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4g_4002/04_2022/5l4g_4002_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4g_4002/04_2022/5l4g_4002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4g_4002/04_2022/5l4g_4002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4g_4002/04_2022/5l4g_4002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4g_4002/04_2022/5l4g_4002_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4g_4002/04_2022/5l4g_4002_trim_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "N PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 46": "OD1" <-> "OD2" Residue "N ASP 58": "OD1" <-> "OD2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N ASP 86": "OD1" <-> "OD2" Residue "N ASP 120": "OD1" <-> "OD2" Residue "N TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 144": "OD1" <-> "OD2" Residue "N TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 155": "OD1" <-> "OD2" Residue "N GLU 180": "OE1" <-> "OE2" Residue "N PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 192": "OE1" <-> "OE2" Residue "N ASP 209": "OD1" <-> "OD2" Residue "N GLU 214": "OE1" <-> "OE2" Residue "N GLU 244": "OE1" <-> "OE2" Residue "N ARG 245": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O GLU 2": "OE1" <-> "OE2" Residue "O ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 48": "OE1" <-> "OE2" Residue "O TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 57": "OD1" <-> "OD2" Residue "O ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O GLU 65": "OE1" <-> "OE2" Residue "O TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 142": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ASP 149": "OD1" <-> "OD2" Residue "O PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O GLU 179": "OE1" <-> "OE2" Residue "O GLU 184": "OE1" <-> "OE2" Residue "O GLU 199": "OE1" <-> "OE2" Residue "O ASP 205": "OD1" <-> "OD2" Residue "O GLU 214": "OE1" <-> "OE2" Residue "O ASP 227": "OD1" <-> "OD2" Residue "O TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 6": "OD1" <-> "OD2" Residue "P GLU 22": "OE1" <-> "OE2" Residue "P GLU 58": "OE1" <-> "OE2" Residue "P PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 82": "OD1" <-> "OD2" Residue "P TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 116": "OD1" <-> "OD2" Residue "P TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 151": "OD1" <-> "OD2" Residue "P GLU 183": "OE1" <-> "OE2" Residue "P ASP 202": "OD1" <-> "OD2" Residue "P GLU 219": "OE1" <-> "OE2" Residue "P GLU 232": "OE1" <-> "OE2" Residue "P GLU 234": "OE1" <-> "OE2" Residue "P GLU 244": "OE1" <-> "OE2" Residue "Q PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 56": "OE1" <-> "OE2" Residue "Q ASP 66": "OD1" <-> "OD2" Residue "Q ASP 67": "OD1" <-> "OD2" Residue "Q GLU 90": "OE1" <-> "OE2" Residue "Q TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ASP 137": "OD1" <-> "OD2" Residue "Q TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 170": "OE1" <-> "OE2" Residue "Q PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ASP 178": "OD1" <-> "OD2" Residue "Q GLU 182": "OE1" <-> "OE2" Residue "Q ASP 184": "OD1" <-> "OD2" Residue "Q GLU 207": "OE1" <-> "OE2" Residue "Q ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 223": "OE1" <-> "OE2" Residue "Q GLU 224": "OE1" <-> "OE2" Residue "Q GLU 238": "OE1" <-> "OE2" Residue "R ASP 9": "OD1" <-> "OD2" Residue "R PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 44": "OE1" <-> "OE2" Residue "R GLU 60": "OE1" <-> "OE2" Residue "R GLU 69": "OE1" <-> "OE2" Residue "R ASP 90": "OD1" <-> "OD2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "R GLU 125": "OE1" <-> "OE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "R PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 147": "OD1" <-> "OD2" Residue "R GLU 148": "OE1" <-> "OE2" Residue "R PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 193": "OE1" <-> "OE2" Residue "R PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 233": "OE1" <-> "OE2" Residue "R GLU 236": "OE1" <-> "OE2" Residue "R ASP 240": "OD1" <-> "OD2" Residue "S ASP 7": "OD1" <-> "OD2" Residue "S GLU 27": "OE1" <-> "OE2" Residue "S PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ASP 100": "OD1" <-> "OD2" Residue "S TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ASP 138": "OD1" <-> "OD2" Residue "S ASP 139": "OD1" <-> "OD2" Residue "S PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ASP 155": "OD1" <-> "OD2" Residue "S TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 181": "OE1" <-> "OE2" Residue "S GLU 197": "OE1" <-> "OE2" Residue "S GLU 220": "OE1" <-> "OE2" Residue "S ASP 225": "OD1" <-> "OD2" Residue "S GLU 237": "OE1" <-> "OE2" Residue "T TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T ASP 43": "OD1" <-> "OD2" Residue "T GLU 50": "OE1" <-> "OE2" Residue "T ASP 70": "OD1" <-> "OD2" Residue "T ASP 83": "OD1" <-> "OD2" Residue "T PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T ASP 152": "OD1" <-> "OD2" Residue "T TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T GLU 175": "OE1" <-> "OE2" Residue "T ASP 188": "OD1" <-> "OD2" Residue "T TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T ASP 202": "OD1" <-> "OD2" Residue "T ASP 206": "OD1" <-> "OD2" Residue "T ARG 223": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T GLU 234": "OE1" <-> "OE2" Residue "T GLU 236": "OE1" <-> "OE2" Residue "T TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T GLU 241": "OE1" <-> "OE2" Residue "U GLU 18": "OE1" <-> "OE2" Residue "U PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ASP 26": "OD1" <-> "OD2" Residue "U ASP 39": "OD1" <-> "OD2" Residue "U TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ASP 48": "OD1" <-> "OD2" Residue "U ASP 60": "OD1" <-> "OD2" Residue "U TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ASP 133": "OD1" <-> "OD2" Residue "U ASP 177": "OD1" <-> "OD2" Residue "U PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ASP 191": "OD1" <-> "OD2" Residue "U GLU 201": "OE1" <-> "OE2" Residue "U GLU 206": "OE1" <-> "OE2" Residue "V GLU 2": "OE1" <-> "OE2" Residue "V ASP 11": "OD1" <-> "OD2" Residue "V ASP 30": "OD1" <-> "OD2" Residue "V ASP 33": "OD1" <-> "OD2" Residue "V PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V GLU 40": "OE1" <-> "OE2" Residue "V TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ASP 90": "OD1" <-> "OD2" Residue "V TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V GLU 109": "OE1" <-> "OE2" Residue "V GLU 111": "OE1" <-> "OE2" Residue "V TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V GLU 154": "OE1" <-> "OE2" Residue "V GLU 165": "OE1" <-> "OE2" Residue "V GLU 166": "OE1" <-> "OE2" Residue "V ASP 190": "OD1" <-> "OD2" Residue "V ASP 192": "OD1" <-> "OD2" Residue "V PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 25": "OD1" <-> "OD2" Residue "W PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 47": "OD1" <-> "OD2" Residue "W ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ASP 59": "OD1" <-> "OD2" Residue "W TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 113": "OD1" <-> "OD2" Residue "W PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 125": "OD1" <-> "OD2" Residue "W ASP 134": "OD1" <-> "OD2" Residue "W ASP 135": "OD1" <-> "OD2" Residue "W GLU 151": "OE1" <-> "OE2" Residue "W PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 165": "OE1" <-> "OE2" Residue "W ASP 176": "OD1" <-> "OD2" Residue "W ASP 178": "OD1" <-> "OD2" Residue "W GLU 191": "OE1" <-> "OE2" Residue "X PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "X GLU 75": "OE1" <-> "OE2" Residue "X ASP 79": "OD1" <-> "OD2" Residue "X ASP 117": "OD1" <-> "OD2" Residue "X PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X GLU 133": "OE1" <-> "OE2" Residue "X GLU 152": "OE1" <-> "OE2" Residue "X GLU 164": "OE1" <-> "OE2" Residue "X GLU 170": "OE1" <-> "OE2" Residue "X ASP 180": "OD1" <-> "OD2" Residue "X GLU 200": "OE1" <-> "OE2" Residue "X GLU 206": "OE1" <-> "OE2" Residue "X ASP 210": "OD1" <-> "OD2" Residue "Y ASP 17": "OD1" <-> "OD2" Residue "Y ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ASP 105": "OD1" <-> "OD2" Residue "Y ASP 146": "OD1" <-> "OD2" Residue "Y ASP 167": "OD1" <-> "OD2" Residue "Y TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y GLU 181": "OE1" <-> "OE2" Residue "Y ASP 190": "OD1" <-> "OD2" Residue "Y GLU 197": "OE1" <-> "OE2" Residue "Z PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ASP 17": "OD1" <-> "OD2" Residue "Z ASP 32": "OD1" <-> "OD2" Residue "Z ASP 39": "OD1" <-> "OD2" Residue "Z ASP 57": "OD1" <-> "OD2" Residue "Z ASP 104": "OD1" <-> "OD2" Residue "Z TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ASP 140": "OD1" <-> "OD2" Residue "Z GLU 150": "OE1" <-> "OE2" Residue "Z GLU 151": "OE1" <-> "OE2" Residue "Z ASP 167": "OD1" <-> "OD2" Residue "Z PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "8 ASP 28": "OD1" <-> "OD2" Residue "8 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "8 ASP 51": "OD1" <-> "OD2" Residue "8 TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "8 TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "8 ASP 104": "OD1" <-> "OD2" Residue "8 TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "8 GLU 139": "OE1" <-> "OE2" Residue "8 ASP 140": "OD1" <-> "OD2" Residue "8 ASP 145": "OD1" <-> "OD2" Residue "8 ASP 166": "OD1" <-> "OD2" Residue "8 ASP 184": "OD1" <-> "OD2" Residue "8 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "8 GLU 205": "OE1" <-> "OE2" Residue "8 GLU 214": "OE1" <-> "OE2" Residue "A ASP 10": "OD1" <-> "OD2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 46": "OD1" <-> "OD2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "B ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 142": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 149": "OD1" <-> "OD2" Residue "B ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 180": "OD1" <-> "OD2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B ASP 185": "OD1" <-> "OD2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ASP 227": "OD1" <-> "OD2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 6": "OD1" <-> "OD2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 151": "OD1" <-> "OD2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C GLU 219": "OE1" <-> "OE2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "D ASP 4": "OD1" <-> "OD2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D ASP 66": "OD1" <-> "OD2" Residue "D TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 147": "OD1" <-> "OD2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 157": "OD1" <-> "OD2" Residue "E ASP 166": "OD1" <-> "OD2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 232": "OE1" <-> "OE2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 138": "OD1" <-> "OD2" Residue "F ASP 139": "OD1" <-> "OD2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 226": "OD1" <-> "OD2" Residue "F ASP 228": "OD1" <-> "OD2" Residue "F GLU 237": "OE1" <-> "OE2" Residue "G ASP 8": "OD1" <-> "OD2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ASP 43": "OD1" <-> "OD2" Residue "G ASP 70": "OD1" <-> "OD2" Residue "G ASP 83": "OD1" <-> "OD2" Residue "G ASP 89": "OD1" <-> "OD2" Residue "G ASP 113": "OD1" <-> "OD2" Residue "G PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G ASP 188": "OD1" <-> "OD2" Residue "G GLU 192": "OE1" <-> "OE2" Residue "G TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "G ARG 223": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 GLU 18": "OE1" <-> "OE2" Residue "1 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 GLU 31": "OE1" <-> "OE2" Residue "1 ASP 39": "OD1" <-> "OD2" Residue "1 TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 ASP 60": "OD1" <-> "OD2" Residue "1 GLU 69": "OE1" <-> "OE2" Residue "1 PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 ASP 114": "OD1" <-> "OD2" Residue "1 TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 ASP 133": "OD1" <-> "OD2" Residue "1 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 ASP 169": "OD1" <-> "OD2" Residue "1 PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 ASP 191": "OD1" <-> "OD2" Residue "2 ASP 11": "OD1" <-> "OD2" Residue "2 ASP 31": "OD1" <-> "OD2" Residue "2 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 GLU 49": "OE1" <-> "OE2" Residue "2 ASP 52": "OD1" <-> "OD2" Residue "2 GLU 58": "OE1" <-> "OE2" Residue "2 TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 GLU 111": "OE1" <-> "OE2" Residue "2 TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 ASP 144": "OD1" <-> "OD2" Residue "2 TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 GLU 154": "OE1" <-> "OE2" Residue "2 GLU 158": "OE1" <-> "OE2" Residue "2 GLU 165": "OE1" <-> "OE2" Residue "3 ASP 25": "OD1" <-> "OD2" Residue "3 ASP 38": "OD1" <-> "OD2" Residue "3 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ASP 59": "OD1" <-> "OD2" Residue "3 GLU 75": "OE1" <-> "OE2" Residue "3 GLU 78": "OE1" <-> "OE2" Residue "3 ASP 113": "OD1" <-> "OD2" Residue "3 ASP 125": "OD1" <-> "OD2" Residue "3 PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 GLU 144": "OE1" <-> "OE2" Residue "3 GLU 151": "OE1" <-> "OE2" Residue "3 ASP 159": "OD1" <-> "OD2" Residue "3 GLU 191": "OE1" <-> "OE2" Residue "3 ASP 193": "OD1" <-> "OD2" Residue "3 ASP 205": "OD1" <-> "OD2" Residue "4 PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 GLU 17": "OE1" <-> "OE2" Residue "4 TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ASP 56": "OD1" <-> "OD2" Residue "4 ASP 59": "OD1" <-> "OD2" Residue "4 ASP 73": "OD1" <-> "OD2" Residue "4 ASP 79": "OD1" <-> "OD2" Residue "4 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 GLU 155": "OE1" <-> "OE2" Residue "4 GLU 194": "OE1" <-> "OE2" Residue "4 GLU 198": "OE1" <-> "OE2" Residue "4 ASP 210": "OD1" <-> "OD2" Residue "5 ASP 17": "OD1" <-> "OD2" Residue "5 GLU 36": "OE1" <-> "OE2" Residue "5 ASP 51": "OD1" <-> "OD2" Residue "5 TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 GLU 72": "OE1" <-> "OE2" Residue "5 TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 GLU 181": "OE1" <-> "OE2" Residue "5 ASP 190": "OD1" <-> "OD2" Residue "5 ASP 194": "OD1" <-> "OD2" Residue "6 ASP 17": "OD1" <-> "OD2" Residue "6 ASP 32": "OD1" <-> "OD2" Residue "6 ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ASP 51": "OD1" <-> "OD2" Residue "6 GLU 72": "OE1" <-> "OE2" Residue "6 GLU 92": "OE1" <-> "OE2" Residue "6 ASP 104": "OD1" <-> "OD2" Residue "6 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 GLU 151": "OE1" <-> "OE2" Residue "6 PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 GLU 165": "OE1" <-> "OE2" Residue "6 GLU 181": "OE1" <-> "OE2" Residue "6 PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 ASP 10": "OD1" <-> "OD2" Residue "7 ASP 17": "OD1" <-> "OD2" Residue "7 ASP 28": "OD1" <-> "OD2" Residue "7 GLU 64": "OE1" <-> "OE2" Residue "7 TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 ASP 104": "OD1" <-> "OD2" Residue "7 TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 ASP 120": "OD1" <-> "OD2" Residue "7 GLU 139": "OE1" <-> "OE2" Residue "7 ASP 140": "OD1" <-> "OD2" Residue "7 ASP 145": "OD1" <-> "OD2" Residue "7 GLU 147": "OE1" <-> "OE2" Residue "7 GLU 148": "OE1" <-> "OE2" Residue "7 GLU 149": "OE1" <-> "OE2" Residue "7 PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 ASP 166": "OD1" <-> "OD2" Residue "7 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 GLU 205": "OE1" <-> "OE2" Residue "7 GLU 214": "OE1" <-> "OE2" Residue "H ASP 50": "OD1" <-> "OD2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H ASP 83": "OD1" <-> "OD2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "H ASP 108": "OD1" <-> "OD2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 124": "OD1" <-> "OD2" Residue "H ASP 133": "OD1" <-> "OD2" Residue "H ASP 143": "OD1" <-> "OD2" Residue "H TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 207": "OE1" <-> "OE2" Residue "H PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 234": "OD1" <-> "OD2" Residue "H PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 252": "OE1" <-> "OE2" Residue "H ASP 275": "OD1" <-> "OD2" Residue "H GLU 276": "OE1" <-> "OE2" Residue "H ASP 292": "OD1" <-> "OD2" Residue "H ASP 325": "OD1" <-> "OD2" Residue "H ASP 328": "OD1" <-> "OD2" Residue "H GLU 365": "OE1" <-> "OE2" Residue "H GLU 371": "OE1" <-> "OE2" Residue "H PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 406": "OE1" <-> "OE2" Residue "H ASP 408": "OD1" <-> "OD2" Residue "H GLU 411": "OE1" <-> "OE2" Residue "H TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 145": "OE1" <-> "OE2" Residue "I ASP 165": "OD1" <-> "OD2" Residue "I ASP 166": "OD1" <-> "OD2" Residue "I ASP 168": "OD1" <-> "OD2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I ASP 186": "OD1" <-> "OD2" Residue "I ASP 191": "OD1" <-> "OD2" Residue "I GLU 199": "OE1" <-> "OE2" Residue "I GLU 202": "OE1" <-> "OE2" Residue "I GLU 209": "OE1" <-> "OE2" Residue "I TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 213": "OE1" <-> "OE2" Residue "I TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 269": "OE1" <-> "OE2" Residue "I GLU 276": "OE1" <-> "OE2" Residue "I ARG 294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 311": "OE1" <-> "OE2" Residue "I ASP 348": "OD1" <-> "OD2" Residue "I GLU 352": "OE1" <-> "OE2" Residue "I ASP 357": "OD1" <-> "OD2" Residue "I ASP 382": "OD1" <-> "OD2" Residue "I ASP 388": "OD1" <-> "OD2" Residue "I GLU 401": "OE1" <-> "OE2" Residue "I GLU 417": "OE1" <-> "OE2" Residue "I ASP 418": "OD1" <-> "OD2" Residue "I TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 77": "OE1" <-> "OE2" Residue "K PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 148": "OD1" <-> "OD2" Residue "K ASP 161": "OD1" <-> "OD2" Residue "K ASP 171": "OD1" <-> "OD2" Residue "K GLU 179": "OE1" <-> "OE2" Residue "K GLU 182": "OE1" <-> "OE2" Residue "K PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 242": "OE1" <-> "OE2" Residue "K PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 256": "OE1" <-> "OE2" Residue "K ASP 265": "OD1" <-> "OD2" Residue "K GLU 266": "OE1" <-> "OE2" Residue "K PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 276": "OD1" <-> "OD2" Residue "K ASP 282": "OD1" <-> "OD2" Residue "K GLU 284": "OE1" <-> "OE2" Residue "K GLU 291": "OE1" <-> "OE2" Residue "K ASP 328": "OD1" <-> "OD2" Residue "K PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 356": "OE1" <-> "OE2" Residue "K GLU 357": "OE1" <-> "OE2" Residue "K TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 368": "OD1" <-> "OD2" Residue "K ASP 374": "OD1" <-> "OD2" Residue "K TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 398": "OD1" <-> "OD2" Residue "K TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 410": "OD1" <-> "OD2" Residue "K TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "L GLU 67": "OE1" <-> "OE2" Residue "L TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 134": "OE1" <-> "OE2" Residue "L GLU 140": "OE1" <-> "OE2" Residue "L GLU 147": "OE1" <-> "OE2" Residue "L PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 210": "OE1" <-> "OE2" Residue "L GLU 217": "OE1" <-> "OE2" Residue "L ASP 236": "OD1" <-> "OD2" Residue "L PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 245": "OE1" <-> "OE2" Residue "L ASP 265": "OD1" <-> "OD2" Residue "L PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 268": "OD1" <-> "OD2" Residue "L ASP 283": "OD1" <-> "OD2" Residue "L ASP 296": "OD1" <-> "OD2" Residue "L GLU 306": "OE1" <-> "OE2" Residue "L TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 336": "OD1" <-> "OD2" Residue "L ASP 342": "OD1" <-> "OD2" Residue "L GLU 349": "OE1" <-> "OE2" Residue "L ASP 358": "OD1" <-> "OD2" Residue "L ASP 385": "OD1" <-> "OD2" Residue "M ASP 27": "OD1" <-> "OD2" Residue "M GLU 40": "OE1" <-> "OE2" Residue "M TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 149": "OD1" <-> "OD2" Residue "M TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 162": "OE1" <-> "OE2" Residue "M ASP 169": "OD1" <-> "OD2" Residue "M GLU 183": "OE1" <-> "OE2" Residue "M TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 192": "OD1" <-> "OD2" Residue "M GLU 200": "OE1" <-> "OE2" Residue "M GLU 213": "OE1" <-> "OE2" Residue "M PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 270": "OD1" <-> "OD2" Residue "M PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 277": "OE1" <-> "OE2" Residue "M ASP 289": "OD1" <-> "OD2" Residue "M PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 297": "OD1" <-> "OD2" Residue "M ASP 303": "OD1" <-> "OD2" Residue "M GLU 312": "OE1" <-> "OE2" Residue "M ASP 318": "OD1" <-> "OD2" Residue "M PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 339": "OD1" <-> "OD2" Residue "M ASP 349": "OD1" <-> "OD2" Residue "M PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 360": "OE1" <-> "OE2" Residue "M GLU 383": "OE1" <-> "OE2" Residue "M ASP 389": "OD1" <-> "OD2" Residue "M ASP 390": "OD1" <-> "OD2" Residue "M PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 402": "OE1" <-> "OE2" Residue "M GLU 414": "OE1" <-> "OE2" Residue "M TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 7": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 68": "OE1" <-> "OE2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "J ASP 98": "OD1" <-> "OD2" Residue "J GLU 141": "OE1" <-> "OE2" Residue "J TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 155": "OD1" <-> "OD2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J ASP 208": "OD1" <-> "OD2" Residue "J PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 233": "OE1" <-> "OE2" Residue "J GLU 240": "OE1" <-> "OE2" Residue "J ASP 252": "OD1" <-> "OD2" Residue "J GLU 260": "OE1" <-> "OE2" Residue "J GLU 275": "OE1" <-> "OE2" Residue "J ASP 302": "OD1" <-> "OD2" Residue "J ASP 312": "OD1" <-> "OD2" Residue "J PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 322": "OE1" <-> "OE2" Residue "J ASP 327": "OD1" <-> "OD2" Residue "J GLU 358": "OE1" <-> "OE2" Residue "J GLU 365": "OE1" <-> "OE2" Residue "J PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 396": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 135488 Number of models: 1 Model: "" Number of chains: 40 Chain: "N" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3814 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain: "O" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3630 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain: "P" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 3963 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 5, 'TRANS': 244} Chain: "Q" Number of atoms: 3875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3875 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 6, 'TRANS': 236} Chain: "R" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3563 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Chain: "S" Number of atoms: 3733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3733 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "T" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3771 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain: "U" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3308 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain: "V" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3197 Classifications: {'peptide': 199} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain: "W" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 3200 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "X" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3358 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "Y" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3080 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "Z" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 2966 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain: "8" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3338 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain: "A" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3814 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain: "B" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3630 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain: "C" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 3963 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 5, 'TRANS': 244} Chain: "D" Number of atoms: 3875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3875 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 6, 'TRANS': 236} Chain: "E" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3563 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Chain: "F" Number of atoms: 3733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3733 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "G" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3764 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 5, 'TRANS': 235} Chain: "1" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3308 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain: "2" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3197 Classifications: {'peptide': 199} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain: "3" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 3200 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "4" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3358 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "5" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3080 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "6" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 2956 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 6, 'TRANS': 192} Chain: "7" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3338 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 8, 'TRANS': 210, 'PCIS': 1} Chain: "H" Number of atoms: 6283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 6283 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 21, 'TRANS': 372, 'PCIS': 2} Chain: "I" Number of atoms: 6043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 6043 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 15, 'TRANS': 361, 'PCIS': 2} Chain: "K" Number of atoms: 6302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 6302 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 373, 'PCIS': 2} Chain: "L" Number of atoms: 6271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 6271 Classifications: {'peptide': 389} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 369, 'PCIS': 1} Chain: "M" Number of atoms: 6575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6575 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 396, 'PCIS': 2} Chain: "J" Number of atoms: 6252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 6252 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 15, 'TRANS': 374, 'PCIS': 1} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 45.76, per 1000 atoms: 0.34 Number of scatterers: 135488 At special positions: 0 Unit cell: (295.65, 163.35, 184.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 399 16.00 P 17 15.00 Mg 5 11.99 O 12953 8.00 N 11666 7.00 C 42652 6.00 H 67796 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 86.29 Conformation dependent library (CDL) restraints added in 8.2 seconds 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15990 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 270 helices and 70 sheets defined 47.0% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 23.93 Creating SS restraints... Processing helix chain 'N' and resid 22 through 36 removed outlier: 3.747A pdb=" N ALA N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS N 30 " --> pdb=" O GLU N 26 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE N 32 " --> pdb=" O ALA N 28 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN N 34 " --> pdb=" O LYS N 30 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY N 35 " --> pdb=" O ALA N 31 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY N 36 " --> pdb=" O ILE N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 removed outlier: 4.138A pdb=" N VAL N 66 " --> pdb=" O ASP N 62 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N THR N 67 " --> pdb=" O SER N 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 67' Processing helix chain 'N' and resid 83 through 106 removed outlier: 3.816A pdb=" N LYS N 102 " --> pdb=" O ALA N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 129 removed outlier: 3.698A pdb=" N VAL N 124 " --> pdb=" O ASP N 120 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR N 125 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR N 126 " --> pdb=" O SER N 122 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ALA N 129 " --> pdb=" O TYR N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 186 removed outlier: 3.791A pdb=" N LYS N 181 " --> pdb=" O SER N 177 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS N 182 " --> pdb=" O PHE N 178 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS N 185 " --> pdb=" O LYS N 181 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS N 186 " --> pdb=" O LYS N 182 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 207 removed outlier: 3.525A pdb=" N THR N 204 " --> pdb=" O THR N 200 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL N 205 " --> pdb=" O CYS N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 216 removed outlier: 3.927A pdb=" N ILE N 215 " --> pdb=" O LYS N 211 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU N 216 " --> pdb=" O PRO N 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 216' Processing helix chain 'N' and resid 231 through 245 removed outlier: 3.594A pdb=" N HIS N 238 " --> pdb=" O GLU N 234 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU N 244 " --> pdb=" O VAL N 240 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG N 245 " --> pdb=" O ALA N 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 36 removed outlier: 4.178A pdb=" N LYS A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 removed outlier: 4.289A pdb=" N VAL A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 67' Processing helix chain 'A' and resid 83 through 106 Processing helix chain 'A' and resid 110 through 129 removed outlier: 3.571A pdb=" N CYS A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ALA A 129 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 186 removed outlier: 3.759A pdb=" N THR A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 207 removed outlier: 3.534A pdb=" N VAL A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.968A pdb=" N ILE A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLU A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 211 through 216' Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.604A pdb=" N ALA A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 32 removed outlier: 3.553A pdb=" N ALA O 26 " --> pdb=" O GLU O 22 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY O 30 " --> pdb=" O ALA O 26 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY O 31 " --> pdb=" O ALA O 27 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA O 32 " --> pdb=" O VAL O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 62 removed outlier: 4.962A pdb=" N VAL O 61 " --> pdb=" O ASP O 57 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N HIS O 62 " --> pdb=" O GLU O 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 57 through 62' Processing helix chain 'O' and resid 78 through 101 removed outlier: 3.518A pdb=" N HIS O 87 " --> pdb=" O ARG O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 123 removed outlier: 3.933A pdb=" N THR O 121 " --> pdb=" O MET O 117 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN O 122 " --> pdb=" O GLN O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 177 removed outlier: 3.598A pdb=" N THR O 171 " --> pdb=" O VAL O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 198 removed outlier: 3.779A pdb=" N GLU O 196 " --> pdb=" O LEU O 192 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SER O 197 " --> pdb=" O THR O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 208 removed outlier: 3.914A pdb=" N ILE O 207 " --> pdb=" O THR O 203 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLU O 208 " --> pdb=" O GLU O 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 203 through 208' Processing helix chain 'O' and resid 221 through 231 Processing helix chain 'B' and resid 18 through 32 removed outlier: 5.530A pdb=" N ALA B 32 " --> pdb=" O VAL B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 removed outlier: 4.662A pdb=" N VAL B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N HIS B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 57 through 62' Processing helix chain 'B' and resid 78 through 101 removed outlier: 3.574A pdb=" N ARG B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 91 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 123 removed outlier: 3.639A pdb=" N SER B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN B 122 " --> pdb=" O GLN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 removed outlier: 3.557A pdb=" N LYS B 170 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 4.461A pdb=" N ALA B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.698A pdb=" N ILE B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 203 through 208' Processing helix chain 'B' and resid 221 through 231 removed outlier: 3.579A pdb=" N TYR B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 7 removed outlier: 4.568A pdb=" N ASP P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N SER P 7 " --> pdb=" O ARG P 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 2 through 7' Processing helix chain 'P' and resid 18 through 31 removed outlier: 3.703A pdb=" N GLU P 26 " --> pdb=" O GLU P 22 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA P 31 " --> pdb=" O ALA P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 101 removed outlier: 3.972A pdb=" N VAL P 85 " --> pdb=" O SER P 81 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN P 88 " --> pdb=" O ASN P 84 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU P 92 " --> pdb=" O ASN P 88 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN P 100 " --> pdb=" O ARG P 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 124 removed outlier: 3.634A pdb=" N VAL P 111 " --> pdb=" O CYS P 107 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE P 117 " --> pdb=" O ALA P 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 179 removed outlier: 3.517A pdb=" N GLN P 177 " --> pdb=" O SER P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 201 removed outlier: 3.522A pdb=" N LEU P 190 " --> pdb=" O LEU P 186 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS P 199 " --> pdb=" O LYS P 195 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 212 removed outlier: 4.300A pdb=" N VAL P 211 " --> pdb=" O SER P 207 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLU P 212 " --> pdb=" O ALA P 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 207 through 212' Processing helix chain 'P' and resid 229 through 250 removed outlier: 3.881A pdb=" N GLU P 242 " --> pdb=" O LYS P 238 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU P 243 " --> pdb=" O LYS P 239 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG P 249 " --> pdb=" O ALA P 245 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLU P 250 " --> pdb=" O LYS P 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 removed outlier: 4.934A pdb=" N ASP C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N SER C 7 " --> pdb=" O ARG C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2 through 7' Processing helix chain 'C' and resid 18 through 31 removed outlier: 3.652A pdb=" N GLU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA C 31 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 101 removed outlier: 3.758A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 124 removed outlier: 3.788A pdb=" N VAL C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.972A pdb=" N GLN C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP C 178 " --> pdb=" O MET C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.584A pdb=" N VAL C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLU C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 212' Processing helix chain 'C' and resid 229 through 250 removed outlier: 3.706A pdb=" N LEU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ARG C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU C 250 " --> pdb=" O LYS C 246 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.558A pdb=" N LYS Q 27 " --> pdb=" O GLN Q 23 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY Q 29 " --> pdb=" O ALA Q 25 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SER Q 30 " --> pdb=" O VAL Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 60 removed outlier: 3.959A pdb=" N VAL Q 59 " --> pdb=" O ASP Q 55 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG Q 60 " --> pdb=" O GLU Q 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 55 through 60' Processing helix chain 'Q' and resid 76 through 98 removed outlier: 3.638A pdb=" N ILE Q 82 " --> pdb=" O ALA Q 78 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 121 removed outlier: 3.935A pdb=" N TYR Q 118 " --> pdb=" O LEU Q 114 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR Q 119 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN Q 120 " --> pdb=" O GLN Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 176 removed outlier: 3.675A pdb=" N VAL Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 182 removed outlier: 5.734A pdb=" N ILE Q 181 " --> pdb=" O THR Q 177 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU Q 182 " --> pdb=" O ASP Q 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 177 through 182' Processing helix chain 'Q' and resid 183 through 199 removed outlier: 3.552A pdb=" N ILE Q 188 " --> pdb=" O ASP Q 184 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS Q 189 " --> pdb=" O ASP Q 185 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU Q 190 " --> pdb=" O LEU Q 186 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU Q 197 " --> pdb=" O LYS Q 193 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL Q 198 " --> pdb=" O ALA Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 221 through 244 removed outlier: 3.501A pdb=" N ILE Q 225 " --> pdb=" O ASN Q 221 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU Q 233 " --> pdb=" O VAL Q 229 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU Q 237 " --> pdb=" O GLU Q 233 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU Q 238 " --> pdb=" O LYS Q 234 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU Q 240 " --> pdb=" O LYS Q 236 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS Q 242 " --> pdb=" O GLU Q 238 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LYS Q 243 " --> pdb=" O ASN Q 239 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN Q 244 " --> pdb=" O GLU Q 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.582A pdb=" N GLN D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER D 30 " --> pdb=" O VAL D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 4.124A pdb=" N VAL D 59 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 55 through 60' Processing helix chain 'D' and resid 76 through 98 removed outlier: 3.591A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG D 95 " --> pdb=" O CYS D 91 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 121 removed outlier: 3.503A pdb=" N THR D 108 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 removed outlier: 4.350A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 removed outlier: 5.158A pdb=" N ILE D 181 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 177 through 182' Processing helix chain 'D' and resid 183 through 199 removed outlier: 3.576A pdb=" N ILE D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 244 removed outlier: 3.618A pdb=" N ILE D 225 " --> pdb=" O ASN D 221 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU D 240 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYS D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS D 242 " --> pdb=" O GLU D 238 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS D 243 " --> pdb=" O ASN D 239 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 35 removed outlier: 3.559A pdb=" N GLU R 29 " --> pdb=" O GLU R 25 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS R 32 " --> pdb=" O ILE R 28 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU R 33 " --> pdb=" O GLU R 29 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLY R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER R 35 " --> pdb=" O ILE R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 65 removed outlier: 4.575A pdb=" N ILE R 64 " --> pdb=" O GLU R 60 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLU R 65 " --> pdb=" O PRO R 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 60 through 65' Processing helix chain 'R' and resid 81 through 103 removed outlier: 3.621A pdb=" N ALA R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS R 86 " --> pdb=" O ILE R 82 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU R 88 " --> pdb=" O ASP R 84 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP R 90 " --> pdb=" O LYS R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 122 removed outlier: 3.730A pdb=" N LEU R 119 " --> pdb=" O ALA R 115 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU R 121 " --> pdb=" O SER R 117 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN R 122 " --> pdb=" O ASN R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 185 removed outlier: 3.589A pdb=" N ALA R 177 " --> pdb=" O ALA R 173 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU R 183 " --> pdb=" O SER R 179 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL R 184 " --> pdb=" O SER R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 206 removed outlier: 3.602A pdb=" N LYS R 196 " --> pdb=" O LYS R 192 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL R 205 " --> pdb=" O ILE R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 216 removed outlier: 3.521A pdb=" N ILE R 215 " --> pdb=" O ASN R 211 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU R 216 " --> pdb=" O ALA R 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 211 through 216' Processing helix chain 'R' and resid 230 through 241 removed outlier: 3.720A pdb=" N LEU R 234 " --> pdb=" O THR R 230 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL R 237 " --> pdb=" O GLU R 233 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP R 240 " --> pdb=" O GLU R 236 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE R 241 " --> pdb=" O VAL R 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 35 removed outlier: 3.962A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 4.423A pdb=" N ILE E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLU E 65 " --> pdb=" O PRO E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 60 through 65' Processing helix chain 'E' and resid 81 through 103 removed outlier: 3.862A pdb=" N ALA E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 122 removed outlier: 4.497A pdb=" N LEU E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLN E 122 " --> pdb=" O ASN E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 185 removed outlier: 3.540A pdb=" N SER E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 184 " --> pdb=" O SER E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 206 removed outlier: 3.594A pdb=" N LYS E 196 " --> pdb=" O LYS E 192 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN E 204 " --> pdb=" O ILE E 200 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 216 removed outlier: 4.679A pdb=" N ILE E 215 " --> pdb=" O ASN E 211 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU E 216 " --> pdb=" O ALA E 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 211 through 216' Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.711A pdb=" N GLU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL E 237 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 33 removed outlier: 3.652A pdb=" N ALA S 25 " --> pdb=" O GLN S 21 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET S 26 " --> pdb=" O ILE S 22 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU S 27 " --> pdb=" O GLU S 23 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA S 28 " --> pdb=" O TYR S 24 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL S 29 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS S 30 " --> pdb=" O MET S 26 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY S 32 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N SER S 33 " --> pdb=" O VAL S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 99 removed outlier: 3.573A pdb=" N LEU S 83 " --> pdb=" O ALA S 79 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG S 96 " --> pdb=" O CYS S 92 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE S 97 " --> pdb=" O LEU S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 123 Proline residue: S 119 - end of helix removed outlier: 4.145A pdb=" N ARG S 122 " --> pdb=" O ILE S 118 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR S 123 " --> pdb=" O PRO S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 164 through 176 removed outlier: 4.018A pdb=" N ALA S 168 " --> pdb=" O ARG S 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 177 through 182 removed outlier: 4.501A pdb=" N GLU S 181 " --> pdb=" O SER S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 183 through 199 removed outlier: 3.552A pdb=" N GLU S 197 " --> pdb=" O ARG S 193 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR S 198 " --> pdb=" O ALA S 194 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU S 199 " --> pdb=" O LEU S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 211 removed outlier: 4.609A pdb=" N VAL S 210 " --> pdb=" O THR S 206 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER S 211 " --> pdb=" O THR S 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 206 through 211' Processing helix chain 'S' and resid 225 through 236 removed outlier: 5.299A pdb=" N VAL S 229 " --> pdb=" O ASP S 225 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER S 230 " --> pdb=" O ASP S 226 " (cutoff:3.500A) Proline residue: S 231 - end of helix removed outlier: 5.149A pdb=" N GLY S 235 " --> pdb=" O PRO S 231 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU S 236 " --> pdb=" O PHE S 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 33 removed outlier: 3.669A pdb=" N MET F 26 " --> pdb=" O ILE F 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER F 33 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 99 removed outlier: 3.515A pdb=" N ASN F 86 " --> pdb=" O ARG F 82 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE F 97 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 123 removed outlier: 3.873A pdb=" N LEU F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Proline residue: F 119 - end of helix removed outlier: 3.653A pdb=" N ARG F 122 " --> pdb=" O ILE F 118 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 176 removed outlier: 4.180A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 182 removed outlier: 5.085A pdb=" N GLU F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS F 182 " --> pdb=" O GLU F 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 177 through 182' Processing helix chain 'F' and resid 183 through 199 removed outlier: 3.501A pdb=" N LYS F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR F 198 " --> pdb=" O ALA F 194 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU F 199 " --> pdb=" O LEU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 211 removed outlier: 4.003A pdb=" N VAL F 210 " --> pdb=" O THR F 206 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER F 211 " --> pdb=" O THR F 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 206 through 211' Processing helix chain 'F' and resid 225 through 236 removed outlier: 4.180A pdb=" N VAL F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER F 230 " --> pdb=" O ASP F 226 " (cutoff:3.500A) Proline residue: F 231 - end of helix removed outlier: 6.050A pdb=" N GLY F 235 " --> pdb=" O PRO F 231 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU F 236 " --> pdb=" O PHE F 232 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 34 removed outlier: 3.698A pdb=" N LYS T 28 " --> pdb=" O GLU T 24 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA T 29 " --> pdb=" O TYR T 25 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL T 30 " --> pdb=" O ALA T 26 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER T 34 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 102 removed outlier: 4.000A pdb=" N ASP T 89 " --> pdb=" O ARG T 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 125 removed outlier: 3.571A pdb=" N ASP T 113 " --> pdb=" O LYS T 109 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR T 122 " --> pdb=" O TYR T 118 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR T 123 " --> pdb=" O VAL T 119 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU T 124 " --> pdb=" O HIS T 120 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TYR T 125 " --> pdb=" O ALA T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 180 removed outlier: 3.623A pdb=" N THR T 174 " --> pdb=" O GLN T 170 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU T 179 " --> pdb=" O GLU T 175 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLN T 180 " --> pdb=" O ILE T 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 201 removed outlier: 4.739A pdb=" N LYS T 191 " --> pdb=" O ARG T 187 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU T 192 " --> pdb=" O ASP T 188 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 207 removed outlier: 5.129A pdb=" N LYS T 207 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing helix chain 'T' and resid 228 through 245 Processing helix chain 'U' and resid 57 through 79 removed outlier: 3.573A pdb=" N THR U 63 " --> pdb=" O GLY U 59 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS U 66 " --> pdb=" O LEU U 62 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS U 73 " --> pdb=" O GLU U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 100 removed outlier: 3.693A pdb=" N THR U 94 " --> pdb=" O ALA U 90 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG U 99 " --> pdb=" O ILE U 95 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG U 100 " --> pdb=" O LEU U 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 141 through 154 removed outlier: 3.536A pdb=" N LEU U 145 " --> pdb=" O ALA U 141 " (cutoff:3.500A) Proline residue: U 147 - end of helix removed outlier: 3.693A pdb=" N ASN U 151 " --> pdb=" O PRO U 147 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY U 154 " --> pdb=" O ASP U 150 " (cutoff:3.500A) Processing helix chain 'U' and resid 167 through 186 removed outlier: 3.566A pdb=" N MET U 172 " --> pdb=" O LEU U 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG U 173 " --> pdb=" O ASP U 169 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU U 184 " --> pdb=" O ILE U 180 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG U 185 " --> pdb=" O SER U 181 " (cutoff:3.500A) Processing helix chain '1' and resid 57 through 79 removed outlier: 3.599A pdb=" N LEU 1 62 " --> pdb=" O HIS 1 58 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR 1 63 " --> pdb=" O GLY 1 59 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS 1 73 " --> pdb=" O GLU 1 69 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR 1 75 " --> pdb=" O ARG 1 71 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER 1 78 " --> pdb=" O MET 1 74 " (cutoff:3.500A) Processing helix chain '1' and resid 84 through 100 removed outlier: 3.783A pdb=" N ALA 1 90 " --> pdb=" O GLY 1 86 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG 1 99 " --> pdb=" O ILE 1 95 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG 1 100 " --> pdb=" O LEU 1 96 " (cutoff:3.500A) Processing helix chain '1' and resid 141 through 154 Proline residue: 1 147 - end of helix Processing helix chain '1' and resid 167 through 186 removed outlier: 3.755A pdb=" N MET 1 172 " --> pdb=" O LEU 1 168 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG 1 173 " --> pdb=" O ASP 1 169 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU 1 184 " --> pdb=" O ILE 1 180 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG 1 185 " --> pdb=" O SER 1 181 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 72 removed outlier: 4.669A pdb=" N VAL V 54 " --> pdb=" O ALA V 50 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN V 55 " --> pdb=" O GLY V 51 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS V 62 " --> pdb=" O GLU V 58 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN V 63 " --> pdb=" O TYR V 59 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR V 67 " --> pdb=" O ASN V 63 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET V 69 " --> pdb=" O GLN V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 95 removed outlier: 3.652A pdb=" N ASN V 87 " --> pdb=" O PHE V 83 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG V 93 " --> pdb=" O ALA V 89 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER V 94 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG V 95 " --> pdb=" O CYS V 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 133 through 147 removed outlier: 4.315A pdb=" N PHE V 137 " --> pdb=" O GLY V 133 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU V 138 " --> pdb=" O TYR V 134 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER V 141 " --> pdb=" O PHE V 137 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE V 142 " --> pdb=" O LEU V 138 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 170 removed outlier: 3.869A pdb=" N VAL V 157 " --> pdb=" O ARG V 153 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN V 168 " --> pdb=" O LEU V 164 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS V 169 " --> pdb=" O GLU V 165 " (cutoff:3.500A) Processing helix chain '2' and resid 49 through 72 removed outlier: 3.785A pdb=" N THR 2 53 " --> pdb=" O GLU 2 49 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL 2 54 " --> pdb=" O ALA 2 50 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE 2 60 " --> pdb=" O PHE 2 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN 2 63 " --> pdb=" O TYR 2 59 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU 2 66 " --> pdb=" O LYS 2 62 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN 2 71 " --> pdb=" O TYR 2 67 " (cutoff:3.500A) Processing helix chain '2' and resid 76 through 95 removed outlier: 3.636A pdb=" N LEU 2 92 " --> pdb=" O LEU 2 88 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG 2 93 " --> pdb=" O ALA 2 89 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER 2 94 " --> pdb=" O ASP 2 90 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARG 2 95 " --> pdb=" O CYS 2 91 " (cutoff:3.500A) Processing helix chain '2' and resid 133 through 147 removed outlier: 4.550A pdb=" N PHE 2 137 " --> pdb=" O GLY 2 133 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU 2 138 " --> pdb=" O TYR 2 134 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER 2 141 " --> pdb=" O PHE 2 137 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE 2 142 " --> pdb=" O LEU 2 138 " (cutoff:3.500A) Processing helix chain '2' and resid 152 through 170 removed outlier: 3.665A pdb=" N LYS 2 162 " --> pdb=" O GLU 2 158 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN 2 168 " --> pdb=" O LEU 2 164 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS 2 169 " --> pdb=" O GLU 2 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 8 removed outlier: 4.703A pdb=" N TYR W 6 " --> pdb=" O SER W 2 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN W 7 " --> pdb=" O ILE W 3 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY W 8 " --> pdb=" O MET W 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 2 through 8' Processing helix chain 'W' and resid 56 through 79 removed outlier: 3.602A pdb=" N ARG W 70 " --> pdb=" O ARG W 66 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU W 73 " --> pdb=" O PHE W 69 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR W 74 " --> pdb=" O ARG W 70 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS W 77 " --> pdb=" O LEU W 73 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU W 78 " --> pdb=" O TYR W 74 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLY W 79 " --> pdb=" O GLU W 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 99 removed outlier: 3.697A pdb=" N SER W 89 " --> pdb=" O TYR W 85 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS W 98 " --> pdb=" O LEU W 94 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG W 99 " --> pdb=" O LEU W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 142 through 154 removed outlier: 3.572A pdb=" N SER W 152 " --> pdb=" O GLY W 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 179 removed outlier: 3.819A pdb=" N PHE W 164 " --> pdb=" O PRO W 160 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU W 165 " --> pdb=" O ASP W 161 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA W 174 " --> pdb=" O ALA W 170 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG W 177 " --> pdb=" O ASN W 173 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP W 178 " --> pdb=" O ALA W 174 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA W 179 " --> pdb=" O VAL W 175 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 8 removed outlier: 5.038A pdb=" N TYR 3 6 " --> pdb=" O SER 3 2 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASN 3 7 " --> pdb=" O ILE 3 3 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY 3 8 " --> pdb=" O MET 3 4 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 2 through 8' Processing helix chain '3' and resid 56 through 79 removed outlier: 3.542A pdb=" N GLN 3 61 " --> pdb=" O ALA 3 57 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG 3 70 " --> pdb=" O ARG 3 66 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS 3 77 " --> pdb=" O LEU 3 73 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY 3 79 " --> pdb=" O GLU 3 75 " (cutoff:3.500A) Processing helix chain '3' and resid 83 through 99 removed outlier: 3.648A pdb=" N MET 3 88 " --> pdb=" O PRO 3 84 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU 3 95 " --> pdb=" O VAL 3 91 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS 3 98 " --> pdb=" O LEU 3 94 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG 3 99 " --> pdb=" O LEU 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 142 through 154 removed outlier: 3.554A pdb=" N GLY 3 148 " --> pdb=" O GLU 3 144 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER 3 152 " --> pdb=" O GLY 3 148 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU 3 153 " --> pdb=" O MET 3 149 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP 3 154 " --> pdb=" O CYS 3 150 " (cutoff:3.500A) Processing helix chain '3' and resid 159 through 179 removed outlier: 3.710A pdb=" N PHE 3 164 " --> pdb=" O PRO 3 160 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN 3 173 " --> pdb=" O GLN 3 169 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG 3 177 " --> pdb=" O ASN 3 173 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP 3 178 " --> pdb=" O ALA 3 174 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA 3 179 " --> pdb=" O VAL 3 175 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 78 removed outlier: 3.536A pdb=" N TYR X 62 " --> pdb=" O ALA X 58 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN X 65 " --> pdb=" O GLN X 61 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY X 68 " --> pdb=" O LYS X 64 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU X 74 " --> pdb=" O MET X 70 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU X 77 " --> pdb=" O ASP X 73 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 103 removed outlier: 3.530A pdb=" N ILE X 88 " --> pdb=" O SER X 84 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER X 90 " --> pdb=" O ARG X 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS X 102 " --> pdb=" O SER X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 146 removed outlier: 4.766A pdb=" N TYR X 144 " --> pdb=" O GLY X 140 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU X 145 " --> pdb=" O TYR X 141 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 157 removed outlier: 4.014A pdb=" N LYS X 156 " --> pdb=" O GLU X 152 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN X 157 " --> pdb=" O VAL X 153 " (cutoff:3.500A) Processing helix chain 'X' and resid 161 through 180 removed outlier: 3.528A pdb=" N ARG X 166 " --> pdb=" O GLN X 162 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP X 167 " --> pdb=" O THR X 163 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS X 172 " --> pdb=" O LEU X 168 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG X 174 " --> pdb=" O GLU X 170 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL X 175 " --> pdb=" O ARG X 171 " (cutoff:3.500A) Processing helix chain 'X' and resid 209 through 215 removed outlier: 4.598A pdb=" N HIS X 213 " --> pdb=" O TRP X 209 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N MET X 214 " --> pdb=" O ASP X 210 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE X 215 " --> pdb=" O ILE X 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 209 through 215' Processing helix chain '4' and resid 56 through 78 removed outlier: 3.699A pdb=" N VAL 4 66 " --> pdb=" O TYR 4 62 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU 4 74 " --> pdb=" O MET 4 70 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU 4 77 " --> pdb=" O ASP 4 73 " (cutoff:3.500A) Processing helix chain '4' and resid 84 through 103 removed outlier: 3.907A pdb=" N MET 4 103 " --> pdb=" O ARG 4 99 " (cutoff:3.500A) Processing helix chain '4' and resid 140 through 146 removed outlier: 4.718A pdb=" N TYR 4 144 " --> pdb=" O GLY 4 140 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU 4 145 " --> pdb=" O TYR 4 141 " (cutoff:3.500A) Processing helix chain '4' and resid 147 through 157 removed outlier: 3.529A pdb=" N LEU 4 154 " --> pdb=" O LEU 4 150 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS 4 156 " --> pdb=" O GLU 4 152 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN 4 157 " --> pdb=" O VAL 4 153 " (cutoff:3.500A) Processing helix chain '4' and resid 161 through 180 removed outlier: 3.627A pdb=" N ARG 4 166 " --> pdb=" O GLN 4 162 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP 4 167 " --> pdb=" O THR 4 163 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG 4 174 " --> pdb=" O GLU 4 170 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL 4 175 " --> pdb=" O ARG 4 171 " (cutoff:3.500A) Processing helix chain '4' and resid 209 through 215 removed outlier: 4.842A pdb=" N HIS 4 213 " --> pdb=" O TRP 4 209 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N MET 4 214 " --> pdb=" O ASP 4 210 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE 4 215 " --> pdb=" O ILE 4 211 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 209 through 215' Processing helix chain 'Y' and resid 48 through 71 removed outlier: 3.581A pdb=" N ILE Y 65 " --> pdb=" O ARG Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 91 removed outlier: 3.609A pdb=" N VAL Y 87 " --> pdb=" O LEU Y 83 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN Y 89 " --> pdb=" O ASN Y 85 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS Y 91 " --> pdb=" O VAL Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 131 through 143 removed outlier: 3.877A pdb=" N GLY Y 137 " --> pdb=" O VAL Y 133 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL Y 138 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY Y 142 " --> pdb=" O VAL Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 167 removed outlier: 3.609A pdb=" N TYR Y 153 " --> pdb=" O VAL Y 149 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP Y 154 " --> pdb=" O GLU Y 150 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA Y 163 " --> pdb=" O ALA Y 159 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 201 removed outlier: 3.677A pdb=" N GLU Y 197 " --> pdb=" O ALA Y 193 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY Y 201 " --> pdb=" O GLU Y 197 " (cutoff:3.500A) Processing helix chain '5' and resid 48 through 71 removed outlier: 3.535A pdb=" N GLU 5 67 " --> pdb=" O CYS 5 63 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU 5 68 " --> pdb=" O ARG 5 64 " (cutoff:3.500A) Processing helix chain '5' and resid 75 through 91 removed outlier: 3.538A pdb=" N ASN 5 85 " --> pdb=" O LYS 5 81 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL 5 87 " --> pdb=" O LEU 5 83 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN 5 89 " --> pdb=" O ASN 5 85 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TYR 5 90 " --> pdb=" O MET 5 86 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS 5 91 " --> pdb=" O VAL 5 87 " (cutoff:3.500A) Processing helix chain '5' and resid 131 through 143 removed outlier: 3.706A pdb=" N GLY 5 137 " --> pdb=" O VAL 5 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL 5 138 " --> pdb=" O TYR 5 134 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY 5 142 " --> pdb=" O VAL 5 138 " (cutoff:3.500A) Processing helix chain '5' and resid 148 through 167 removed outlier: 3.710A pdb=" N TYR 5 153 " --> pdb=" O VAL 5 149 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP 5 154 " --> pdb=" O GLU 5 150 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA 5 163 " --> pdb=" O ALA 5 159 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG 5 166 " --> pdb=" O GLN 5 162 " (cutoff:3.500A) Processing helix chain '5' and resid 191 through 201 removed outlier: 3.723A pdb=" N GLU 5 197 " --> pdb=" O ALA 5 193 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY 5 201 " --> pdb=" O GLU 5 197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 71 removed outlier: 3.608A pdb=" N ASP Z 57 " --> pdb=" O GLN Z 53 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN Z 62 " --> pdb=" O ALA Z 58 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU Z 70 " --> pdb=" O HIS Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 91 removed outlier: 4.070A pdb=" N PHE Z 83 " --> pdb=" O ALA Z 79 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR Z 88 " --> pdb=" O LYS Z 84 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG Z 91 " --> pdb=" O CYS Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 4.072A pdb=" N ILE Z 135 " --> pdb=" O GLY Z 131 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR Z 136 " --> pdb=" O SER Z 132 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY Z 137 " --> pdb=" O SER Z 133 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N TYR Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP Z 140 " --> pdb=" O TYR Z 136 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR Z 143 " --> pdb=" O VAL Z 139 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 167 removed outlier: 3.590A pdb=" N PHE Z 155 " --> pdb=" O GLU Z 151 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG Z 166 " --> pdb=" O LEU Z 162 " (cutoff:3.500A) Processing helix chain '8' and resid 48 through 71 removed outlier: 3.528A pdb=" N ASP 8 53 " --> pdb=" O ALA 8 49 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET 8 54 " --> pdb=" O ALA 8 50 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU 8 58 " --> pdb=" O MET 8 54 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU 8 65 " --> pdb=" O SER 8 61 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER 8 69 " --> pdb=" O LEU 8 65 " (cutoff:3.500A) Processing helix chain '8' and resid 75 through 91 removed outlier: 3.850A pdb=" N ALA 8 79 " --> pdb=" O ARG 8 75 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG 8 89 " --> pdb=" O GLN 8 85 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR 8 90 " --> pdb=" O MET 8 86 " (cutoff:3.500A) Processing helix chain '8' and resid 130 through 141 removed outlier: 3.865A pdb=" N VAL 8 137 " --> pdb=" O ALA 8 133 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP 8 140 " --> pdb=" O ALA 8 136 " (cutoff:3.500A) Processing helix chain '8' and resid 147 through 166 removed outlier: 3.745A pdb=" N ASP 8 166 " --> pdb=" O GLY 8 162 " (cutoff:3.500A) Processing helix chain '7' and resid 48 through 71 removed outlier: 3.845A pdb=" N MET 7 54 " --> pdb=" O ALA 7 50 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU 7 58 " --> pdb=" O MET 7 54 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS 7 66 " --> pdb=" O ASN 7 62 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU 7 68 " --> pdb=" O GLU 7 64 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER 7 69 " --> pdb=" O LEU 7 65 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR 7 70 " --> pdb=" O HIS 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 75 through 91 removed outlier: 3.639A pdb=" N ALA 7 79 " --> pdb=" O ARG 7 75 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS 7 84 " --> pdb=" O ASN 7 80 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG 7 89 " --> pdb=" O GLN 7 85 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR 7 90 " --> pdb=" O MET 7 86 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN 7 91 " --> pdb=" O LEU 7 87 " (cutoff:3.500A) Processing helix chain '7' and resid 130 through 141 removed outlier: 3.507A pdb=" N VAL 7 137 " --> pdb=" O ALA 7 133 " (cutoff:3.500A) Processing helix chain '7' and resid 147 through 166 removed outlier: 3.608A pdb=" N LYS 7 152 " --> pdb=" O GLU 7 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 34 removed outlier: 3.566A pdb=" N GLU G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 102 removed outlier: 3.602A pdb=" N ASP G 89 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG G 99 " --> pdb=" O ALA G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 125 removed outlier: 4.055A pdb=" N TYR G 122 " --> pdb=" O TYR G 118 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR G 123 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU G 124 " --> pdb=" O HIS G 120 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N TYR G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 180 removed outlier: 3.550A pdb=" N THR G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU G 179 " --> pdb=" O GLU G 175 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLN G 180 " --> pdb=" O ILE G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 202 removed outlier: 3.529A pdb=" N VAL G 190 " --> pdb=" O CYS G 186 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU G 192 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASP G 202 " --> pdb=" O TYR G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 245 removed outlier: 3.716A pdb=" N SER G 242 " --> pdb=" O TYR G 238 " (cutoff:3.500A) Processing helix chain '6' and resid 48 through 71 removed outlier: 3.563A pdb=" N GLN 6 53 " --> pdb=" O ALA 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 75 through 91 removed outlier: 3.659A pdb=" N PHE 6 83 " --> pdb=" O ALA 6 79 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG 6 91 " --> pdb=" O CYS 6 87 " (cutoff:3.500A) Processing helix chain '6' and resid 131 through 143 removed outlier: 4.382A pdb=" N ILE 6 135 " --> pdb=" O GLY 6 131 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR 6 136 " --> pdb=" O SER 6 132 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLY 6 137 " --> pdb=" O SER 6 133 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR 6 138 " --> pdb=" O TYR 6 134 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR 6 143 " --> pdb=" O VAL 6 139 " (cutoff:3.500A) Processing helix chain '6' and resid 148 through 167 removed outlier: 3.925A pdb=" N GLN 6 154 " --> pdb=" O GLU 6 150 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA 6 157 " --> pdb=" O LEU 6 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 63 removed outlier: 3.536A pdb=" N GLN H 47 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 89 removed outlier: 4.261A pdb=" N LEU H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU H 87 " --> pdb=" O ASP H 83 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N SER H 89 " --> pdb=" O GLN H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 166 removed outlier: 4.459A pdb=" N MET H 164 " --> pdb=" O THR H 160 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN H 165 " --> pdb=" O VAL H 161 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL H 166 " --> pdb=" O THR H 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 160 through 166' Processing helix chain 'H' and resid 173 through 178 removed outlier: 4.189A pdb=" N VAL H 177 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLY H 178 " --> pdb=" O TYR H 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 173 through 178' Processing helix chain 'H' and resid 181 through 197 removed outlier: 3.595A pdb=" N LEU H 187 " --> pdb=" O GLN H 183 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR H 193 " --> pdb=" O GLU H 189 " (cutoff:3.500A) Proline residue: H 194 - end of helix Processing helix chain 'H' and resid 198 through 205 removed outlier: 3.853A pdb=" N VAL H 202 " --> pdb=" O PRO H 198 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU H 204 " --> pdb=" O ARG H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 233 removed outlier: 3.790A pdb=" N ASN H 231 " --> pdb=" O ARG H 227 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG H 232 " --> pdb=" O ALA H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 247 removed outlier: 3.966A pdb=" N LEU H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL H 246 " --> pdb=" O GLY H 242 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLN H 247 " --> pdb=" O SER H 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 241 through 247' Processing helix chain 'H' and resid 251 through 268 removed outlier: 3.741A pdb=" N THR H 266 " --> pdb=" O GLU H 262 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS H 267 " --> pdb=" O MET H 263 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS H 268 " --> pdb=" O ALA H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 308 removed outlier: 3.626A pdb=" N ASP H 307 " --> pdb=" O ILE H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 333 Processing helix chain 'H' and resid 347 through 363 removed outlier: 3.501A pdb=" N LYS H 356 " --> pdb=" O THR H 352 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N SER H 361 " --> pdb=" O ILE H 357 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N MET H 362 " --> pdb=" O HIS H 358 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N SER H 363 " --> pdb=" O ALA H 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 378 Proline residue: H 378 - end of helix Processing helix chain 'H' and resid 381 through 400 Processing helix chain 'H' and resid 405 through 424 removed outlier: 3.548A pdb=" N PHE H 409 " --> pdb=" O THR H 405 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER H 419 " --> pdb=" O LYS H 415 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR H 420 " --> pdb=" O VAL H 416 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS H 422 " --> pdb=" O LYS H 418 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE H 423 " --> pdb=" O SER H 419 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER H 424 " --> pdb=" O TYR H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 425 through 433 removed outlier: 4.664A pdb=" N THR H 431 " --> pdb=" O PRO H 427 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR H 432 " --> pdb=" O ARG H 428 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN H 433 " --> pdb=" O TYR H 429 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 84 removed outlier: 4.128A pdb=" N LYS I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG I 67 " --> pdb=" O LEU I 63 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 104 Processing helix chain 'I' and resid 140 through 145 removed outlier: 4.077A pdb=" N LEU I 144 " --> pdb=" O ASP I 140 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLU I 145 " --> pdb=" O LYS I 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 140 through 145' Processing helix chain 'I' and resid 168 through 175 removed outlier: 4.405A pdb=" N THR I 172 " --> pdb=" O ASP I 168 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL I 173 " --> pdb=" O PRO I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 188 removed outlier: 3.911A pdb=" N ILE I 187 " --> pdb=" O THR I 183 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLY I 188 " --> pdb=" O TYR I 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 183 through 188' Processing helix chain 'I' and resid 190 through 201 removed outlier: 3.974A pdb=" N ILE I 194 " --> pdb=" O LEU I 190 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE I 197 " --> pdb=" O GLN I 193 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS I 198 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU I 199 " --> pdb=" O GLN I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 207 Processing helix chain 'I' and resid 208 through 215 removed outlier: 3.660A pdb=" N GLU I 212 " --> pdb=" O PRO I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 231 through 244 removed outlier: 4.333A pdb=" N SER I 244 " --> pdb=" O ALA I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 256 removed outlier: 4.145A pdb=" N LEU I 255 " --> pdb=" O VAL I 251 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE I 256 " --> pdb=" O GLY I 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 251 through 256' Processing helix chain 'I' and resid 261 through 278 removed outlier: 3.553A pdb=" N PHE I 271 " --> pdb=" O VAL I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 292 removed outlier: 4.757A pdb=" N ILE I 290 " --> pdb=" O GLU I 286 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY I 291 " --> pdb=" O ILE I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 318 removed outlier: 3.571A pdb=" N ASP I 317 " --> pdb=" O LEU I 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 343 removed outlier: 3.831A pdb=" N ILE I 342 " --> pdb=" O ASP I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 357 through 371 removed outlier: 3.757A pdb=" N THR I 369 " --> pdb=" O PHE I 365 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER I 370 " --> pdb=" O GLN I 366 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG I 371 " --> pdb=" O ILE I 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 379 through 388 removed outlier: 3.614A pdb=" N LEU I 383 " --> pdb=" O THR I 379 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET I 385 " --> pdb=" O ASP I 381 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS I 387 " --> pdb=" O LEU I 383 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP I 388 " --> pdb=" O ILE I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 391 through 410 removed outlier: 3.621A pdb=" N GLU I 409 " --> pdb=" O MET I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 434 removed outlier: 3.625A pdb=" N TYR I 428 " --> pdb=" O GLU I 424 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS I 429 " --> pdb=" O ASN I 425 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY I 433 " --> pdb=" O LYS I 429 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N THR I 434 " --> pdb=" O LYS I 430 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 76 removed outlier: 3.589A pdb=" N GLN K 57 " --> pdb=" O PHE K 53 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS K 62 " --> pdb=" O GLU K 58 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 84 removed outlier: 4.713A pdb=" N GLN K 83 " --> pdb=" O VAL K 79 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER K 84 " --> pdb=" O LYS K 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 79 through 84' Processing helix chain 'K' and resid 120 through 126 removed outlier: 3.803A pdb=" N LEU K 124 " --> pdb=" O ASP K 120 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LYS K 125 " --> pdb=" O ARG K 121 " (cutoff:3.500A) Proline residue: K 126 - end of helix No H-bonds generated for 'chain 'K' and resid 120 through 126' Processing helix chain 'K' and resid 163 through 168 removed outlier: 4.462A pdb=" N ILE K 167 " --> pdb=" O MET K 163 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLY K 168 " --> pdb=" O TYR K 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 163 through 168' Processing helix chain 'K' and resid 170 through 187 removed outlier: 3.661A pdb=" N ARG K 178 " --> pdb=" O LYS K 174 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU K 183 " --> pdb=" O GLU K 179 " (cutoff:3.500A) Proline residue: K 184 - end of helix Processing helix chain 'K' and resid 188 through 195 removed outlier: 3.620A pdb=" N LYS K 192 " --> pdb=" O PHE K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 223 removed outlier: 3.582A pdb=" N HIS K 221 " --> pdb=" O LYS K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 258 removed outlier: 3.734A pdb=" N ARG K 245 " --> pdb=" O GLY K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 300 removed outlier: 3.588A pdb=" N VAL K 285 " --> pdb=" O ALA K 281 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP K 297 " --> pdb=" O LEU K 293 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE K 299 " --> pdb=" O GLN K 295 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP K 300 " --> pdb=" O MET K 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 318 removed outlier: 3.648A pdb=" N LEU K 317 " --> pdb=" O ARG K 313 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ASP K 318 " --> pdb=" O ALA K 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 313 through 318' Processing helix chain 'K' and resid 337 through 353 removed outlier: 3.883A pdb=" N LYS K 351 " --> pdb=" O THR K 347 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET K 352 " --> pdb=" O ILE K 348 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN K 353 " --> pdb=" O THR K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 367 removed outlier: 3.873A pdb=" N TYR K 363 " --> pdb=" O ASP K 359 " (cutoff:3.500A) Proline residue: K 367 - end of helix Processing helix chain 'K' and resid 371 through 390 removed outlier: 3.551A pdb=" N ASN K 376 " --> pdb=" O GLY K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 412 removed outlier: 3.731A pdb=" N GLU K 400 " --> pdb=" O ALA K 396 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR K 403 " --> pdb=" O PHE K 399 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL K 406 " --> pdb=" O ALA K 402 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS K 408 " --> pdb=" O LYS K 404 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS K 409 " --> pdb=" O THR K 405 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP K 410 " --> pdb=" O VAL K 406 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLN K 412 " --> pdb=" O LYS K 408 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 52 removed outlier: 3.657A pdb=" N GLU L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER L 43 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU L 47 " --> pdb=" O SER L 43 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN L 51 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER L 52 " --> pdb=" O LYS L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 93 removed outlier: 3.819A pdb=" N LEU L 92 " --> pdb=" O ASP L 88 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LYS L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 88 through 93' Processing helix chain 'L' and resid 116 through 125 Processing helix chain 'L' and resid 131 through 136 removed outlier: 3.786A pdb=" N ILE L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLY L 136 " --> pdb=" O TYR L 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 131 through 136' Processing helix chain 'L' and resid 138 through 155 removed outlier: 5.154A pdb=" N ILE L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU L 151 " --> pdb=" O GLU L 147 " (cutoff:3.500A) Proline residue: L 152 - end of helix Processing helix chain 'L' and resid 156 through 163 removed outlier: 3.565A pdb=" N GLN L 160 " --> pdb=" O PRO L 156 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL L 162 " --> pdb=" O LEU L 158 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 191 removed outlier: 3.565A pdb=" N ALA L 184 " --> pdb=" O LYS L 180 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN L 190 " --> pdb=" O ALA L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 204 removed outlier: 3.937A pdb=" N ILE L 203 " --> pdb=" O VAL L 199 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL L 204 " --> pdb=" O SER L 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 199 through 204' Processing helix chain 'L' and resid 209 through 226 removed outlier: 4.866A pdb=" N ARG L 213 " --> pdb=" O GLY L 209 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU L 214 " --> pdb=" O GLU L 210 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE L 215 " --> pdb=" O SER L 211 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA L 222 " --> pdb=" O MET L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 235 through 240 removed outlier: 4.077A pdb=" N GLY L 240 " --> pdb=" O ASP L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 266 removed outlier: 3.916A pdb=" N ARG L 255 " --> pdb=" O ARG L 251 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR L 256 " --> pdb=" O GLU L 252 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP L 265 " --> pdb=" O LEU L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 291 Processing helix chain 'L' and resid 305 through 318 removed outlier: 6.195A pdb=" N ASP L 311 " --> pdb=" O GLN L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 336 removed outlier: 4.575A pdb=" N ASP L 336 " --> pdb=" O VAL L 332 " (cutoff:3.500A) Processing helix chain 'L' and resid 339 through 358 removed outlier: 3.708A pdb=" N ALA L 354 " --> pdb=" O ALA L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 363 through 382 removed outlier: 3.781A pdb=" N PHE L 367 " --> pdb=" O VAL L 363 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER L 382 " --> pdb=" O LYS L 378 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 36 Processing helix chain 'M' and resid 37 through 85 removed outlier: 3.545A pdb=" N ILE M 42 " --> pdb=" O THR M 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU M 47 " --> pdb=" O GLN M 43 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER M 50 " --> pdb=" O ARG M 46 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU M 51 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LYS M 53 " --> pdb=" O ASP M 49 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ILE M 54 " --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET M 55 " --> pdb=" O GLU M 51 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS M 70 " --> pdb=" O LEU M 66 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU M 75 " --> pdb=" O ASP M 71 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR M 85 " --> pdb=" O LYS M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 121 removed outlier: 3.593A pdb=" N SER M 115 " --> pdb=" O ILE M 111 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN M 116 " --> pdb=" O ASP M 112 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG M 117 " --> pdb=" O LEU M 113 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N CYS M 121 " --> pdb=" O ARG M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 176 removed outlier: 4.323A pdb=" N GLU M 176 " --> pdb=" O VAL M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 189 removed outlier: 4.109A pdb=" N ILE M 188 " --> pdb=" O GLN M 184 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLY M 189 " --> pdb=" O TYR M 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 184 through 189' Processing helix chain 'M' and resid 191 through 208 removed outlier: 3.608A pdb=" N ILE M 195 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA M 201 " --> pdb=" O GLU M 197 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU M 204 " --> pdb=" O GLU M 200 " (cutoff:3.500A) Proline residue: M 205 - end of helix Processing helix chain 'M' and resid 209 through 216 removed outlier: 3.575A pdb=" N LEU M 215 " --> pdb=" O LYS M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 245 removed outlier: 4.637A pdb=" N LYS M 245 " --> pdb=" O ALA M 241 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 258 removed outlier: 4.168A pdb=" N LEU M 256 " --> pdb=" O ALA M 252 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL M 257 " --> pdb=" O GLY M 253 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLN M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 252 through 258' Processing helix chain 'M' and resid 262 through 279 removed outlier: 3.543A pdb=" N VAL M 268 " --> pdb=" O GLY M 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 303 through 318 removed outlier: 6.374A pdb=" N GLN M 307 " --> pdb=" O ASP M 303 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ARG M 308 " --> pdb=" O ARG M 304 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU M 313 " --> pdb=" O THR M 309 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN M 315 " --> pdb=" O LEU M 311 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP M 318 " --> pdb=" O LEU M 314 " (cutoff:3.500A) Processing helix chain 'M' and resid 339 through 344 removed outlier: 3.617A pdb=" N LEU M 343 " --> pdb=" O ASP M 339 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG M 344 " --> pdb=" O PRO M 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 339 through 344' Processing helix chain 'M' and resid 358 through 374 removed outlier: 3.567A pdb=" N HIS M 369 " --> pdb=" O ILE M 365 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG M 371 " --> pdb=" O GLN M 367 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LYS M 372 " --> pdb=" O ILE M 368 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N MET M 373 " --> pdb=" O HIS M 369 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASN M 374 " --> pdb=" O SER M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 380 through 389 removed outlier: 4.879A pdb=" N ASP M 389 " --> pdb=" O ALA M 385 " (cutoff:3.500A) Processing helix chain 'M' and resid 392 through 411 removed outlier: 3.538A pdb=" N CYS M 400 " --> pdb=" O CYS M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 428 removed outlier: 3.731A pdb=" N TYR M 420 " --> pdb=" O THR M 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 68 removed outlier: 3.542A pdb=" N TYR J 24 " --> pdb=" O LEU J 20 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN J 64 " --> pdb=" O ARG J 60 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU J 65 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLN J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU J 68 " --> pdb=" O GLN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 109 removed outlier: 3.865A pdb=" N VAL J 108 " --> pdb=" O ASP J 104 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N THR J 109 " --> pdb=" O ILE J 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 104 through 109' Processing helix chain 'J' and resid 132 through 142 removed outlier: 3.547A pdb=" N MET J 138 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET J 139 " --> pdb=" O VAL J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 152 removed outlier: 3.617A pdb=" N ILE J 151 " --> pdb=" O THR J 147 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY J 152 " --> pdb=" O TYR J 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 147 through 152' Processing helix chain 'J' and resid 154 through 171 removed outlier: 4.868A pdb=" N ILE J 158 " --> pdb=" O LEU J 154 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU J 163 " --> pdb=" O LYS J 159 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU J 167 " --> pdb=" O GLU J 163 " (cutoff:3.500A) Proline residue: J 168 - end of helix Processing helix chain 'J' and resid 172 through 179 Processing helix chain 'J' and resid 195 through 208 Processing helix chain 'J' and resid 217 through 225 removed outlier: 3.715A pdb=" N GLN J 221 " --> pdb=" O SER J 217 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE J 223 " --> pdb=" O LEU J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 242 removed outlier: 4.129A pdb=" N GLU J 233 " --> pdb=" O ARG J 229 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU J 234 " --> pdb=" O MET J 230 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE J 235 " --> pdb=" O VAL J 231 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET J 237 " --> pdb=" O GLU J 233 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU J 240 " --> pdb=" O VAL J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 261 removed outlier: 4.724A pdb=" N LEU J 259 " --> pdb=" O GLY J 255 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU J 260 " --> pdb=" O SER J 256 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLY J 261 " --> pdb=" O SER J 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 255 through 261' Processing helix chain 'J' and resid 266 through 280 removed outlier: 4.463A pdb=" N GLN J 270 " --> pdb=" O ASP J 266 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG J 271 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET J 273 " --> pdb=" O VAL J 269 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU J 275 " --> pdb=" O ARG J 271 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN J 278 " --> pdb=" O LEU J 274 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLN J 279 " --> pdb=" O GLU J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 307 removed outlier: 3.598A pdb=" N LEU J 306 " --> pdb=" O ASP J 302 " (cutoff:3.500A) Processing helix chain 'J' and resid 321 through 337 removed outlier: 3.613A pdb=" N HIS J 332 " --> pdb=" O ILE J 328 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG J 334 " --> pdb=" O LYS J 330 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS J 335 " --> pdb=" O ILE J 331 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N MET J 336 " --> pdb=" O HIS J 332 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN J 337 " --> pdb=" O SER J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 352 Proline residue: J 352 - end of helix Processing helix chain 'J' and resid 355 through 374 removed outlier: 3.874A pdb=" N VAL J 359 " --> pdb=" O SER J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 397 removed outlier: 3.604A pdb=" N ALA J 388 " --> pdb=" O GLU J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 286 removed outlier: 4.415A pdb=" N GLU J 284 " --> pdb=" O ASP J 281 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA J 285 " --> pdb=" O GLY J 282 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'N' and resid 68 through 72 removed outlier: 5.990A pdb=" N HIS N 68 " --> pdb=" O MET N 80 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE N 70 " --> pdb=" O CYS N 78 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE N 76 " --> pdb=" O ILE N 72 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET N 138 " --> pdb=" O CYS N 154 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL N 151 " --> pdb=" O PHE N 163 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS N 153 " --> pdb=" O CYS N 161 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS N 161 " --> pdb=" O LYS N 153 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP N 155 " --> pdb=" O TYR N 159 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR N 159 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'N' and resid 165 through 169 removed outlier: 4.801A pdb=" N VAL N 217 " --> pdb=" O LEU N 230 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 68 through 72 removed outlier: 6.042A pdb=" N HIS A 68 " --> pdb=" O MET A 80 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL A 151 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N TYR A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 165 through 169 removed outlier: 4.725A pdb=" N VAL A 217 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'O' and resid 64 through 67 removed outlier: 6.559A pdb=" N ILE O 71 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N HIS O 70 " --> pdb=" O TRP O 138 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP O 138 " --> pdb=" O HIS O 70 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU O 145 " --> pdb=" O TRP O 157 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'O' and resid 159 through 163 removed outlier: 5.454A pdb=" N VAL O 209 " --> pdb=" O LEU O 220 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE O 211 " --> pdb=" O ARG O 218 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN O 213 " --> pdb=" O GLY O 216 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 64 through 67 removed outlier: 3.524A pdb=" N ILE B 67 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N HIS B 70 " --> pdb=" O TRP B 138 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B 138 " --> pdb=" O HIS B 70 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B 145 " --> pdb=" O TRP B 157 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 159 through 163 removed outlier: 5.375A pdb=" N VAL B 209 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN B 213 " --> pdb=" O GLY B 216 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'P' and resid 64 through 68 removed outlier: 6.695A pdb=" N LYS P 64 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N MET P 72 " --> pdb=" O LEU P 68 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU P 147 " --> pdb=" O TRP P 159 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN P 155 " --> pdb=" O ASP P 151 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'P' and resid 161 through 165 removed outlier: 5.108A pdb=" N THR P 33 " --> pdb=" O GLU P 48 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU P 44 " --> pdb=" O ILE P 37 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 64 through 68 removed outlier: 7.302A pdb=" N LYS C 64 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 76 " --> pdb=" O LYS C 64 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU C 147 " --> pdb=" O TRP C 159 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASN C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 161 through 165 removed outlier: 5.075A pdb=" N THR C 33 " --> pdb=" O GLU C 48 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'Q' and resid 62 through 65 removed outlier: 6.742A pdb=" N VAL Q 69 " --> pdb=" O LEU Q 65 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASN Q 68 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU Q 144 " --> pdb=" O TRP Q 156 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR Q 152 " --> pdb=" O ASP Q 148 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'Q' and resid 158 through 162 removed outlier: 5.156A pdb=" N THR Q 31 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 62 through 65 removed outlier: 6.834A pdb=" N VAL D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASN D 68 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 131 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU D 144 " --> pdb=" O TRP D 156 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP D 148 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 158 through 162 removed outlier: 4.620A pdb=" N THR D 31 " --> pdb=" O GLU D 46 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'R' and resid 67 through 70 removed outlier: 6.441A pdb=" N ILE R 74 " --> pdb=" O ILE R 70 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N HIS R 73 " --> pdb=" O VAL R 146 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'R' and resid 167 through 171 removed outlier: 5.376A pdb=" N LEU R 217 " --> pdb=" O PHE R 229 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'E' and resid 67 through 70 removed outlier: 6.462A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS E 73 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'E' and resid 167 through 171 removed outlier: 4.990A pdb=" N LEU E 217 " --> pdb=" O PHE E 229 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'S' and resid 63 through 66 removed outlier: 4.028A pdb=" N VAL S 66 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE S 70 " --> pdb=" O VAL S 66 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS S 69 " --> pdb=" O TYR S 137 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY S 141 " --> pdb=" O ASP S 138 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE S 144 " --> pdb=" O CYS S 156 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN S 152 " --> pdb=" O CYS S 148 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'S' and resid 158 through 162 removed outlier: 4.680A pdb=" N ALA S 34 " --> pdb=" O LEU S 49 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'F' and resid 63 through 66 removed outlier: 6.682A pdb=" N ILE F 70 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N HIS F 69 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY F 141 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE F 144 " --> pdb=" O CYS F 156 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS F 148 " --> pdb=" O ASN F 152 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN F 152 " --> pdb=" O CYS F 148 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'F' and resid 158 through 162 removed outlier: 4.580A pdb=" N ALA F 34 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE F 214 " --> pdb=" O THR F 222 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'T' and resid 65 through 69 removed outlier: 6.576A pdb=" N ARG T 65 " --> pdb=" O VAL T 77 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL T 73 " --> pdb=" O VAL T 69 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU T 148 " --> pdb=" O TYR T 160 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR T 158 " --> pdb=" O MET T 150 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL T 156 " --> pdb=" O ASP T 152 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'T' and resid 162 through 166 removed outlier: 4.519A pdb=" N THR T 35 " --> pdb=" O GLU T 50 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL T 53 " --> pdb=" O ALA T 208 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA T 208 " --> pdb=" O VAL T 53 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'U' and resid 43 through 46 removed outlier: 6.902A pdb=" N THR U 50 " --> pdb=" O LEU U 46 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASN U 108 " --> pdb=" O PHE U 124 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'U' and resid 135 through 139 removed outlier: 5.279A pdb=" N THR U 11 " --> pdb=" O ASP U 26 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA U 192 " --> pdb=" O THR U 27 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP U 191 " --> pdb=" O LEU U 210 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU U 210 " --> pdb=" O ASP U 191 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE U 195 " --> pdb=" O GLU U 206 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR U 199 " --> pdb=" O GLY U 202 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '1' and resid 43 through 46 removed outlier: 6.726A pdb=" N THR 1 50 " --> pdb=" O LEU 1 46 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN 1 108 " --> pdb=" O PHE 1 124 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '1' and resid 135 through 139 removed outlier: 5.381A pdb=" N THR 1 11 " --> pdb=" O ASP 1 26 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR 1 27 " --> pdb=" O ALA 1 192 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA 1 192 " --> pdb=" O THR 1 27 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASP 1 191 " --> pdb=" O LEU 1 210 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU 1 210 " --> pdb=" O ASP 1 191 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR 1 199 " --> pdb=" O GLY 1 202 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY 1 202 " --> pdb=" O THR 1 199 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'V' and resid 35 through 38 removed outlier: 6.941A pdb=" N ILE V 42 " --> pdb=" O MET V 38 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LYS V 41 " --> pdb=" O TYR V 107 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'V' and resid 129 through 132 removed outlier: 3.729A pdb=" N LEU V 4 " --> pdb=" O HIS V 132 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR V 3 " --> pdb=" O ASP V 18 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '2' and resid 35 through 38 removed outlier: 3.583A pdb=" N LEU 2 44 " --> pdb=" O PHE 2 36 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE 2 42 " --> pdb=" O MET 2 38 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LYS 2 41 " --> pdb=" O TYR 2 107 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '2' and resid 129 through 132 removed outlier: 3.987A pdb=" N LEU 2 4 " --> pdb=" O HIS 2 132 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR 2 3 " --> pdb=" O ASP 2 18 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'W' and resid 42 through 45 removed outlier: 5.448A pdb=" N LEU W 49 " --> pdb=" O MET W 45 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARG W 48 " --> pdb=" O LEU W 112 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA W 54 " --> pdb=" O GLU W 106 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'W' and resid 136 through 140 removed outlier: 5.593A pdb=" N ALA W 10 " --> pdb=" O ASP W 25 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL W 185 " --> pdb=" O LEU W 200 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS W 194 " --> pdb=" O GLU W 191 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain '3' and resid 42 through 45 removed outlier: 5.012A pdb=" N LEU 3 49 " --> pdb=" O MET 3 45 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ARG 3 48 " --> pdb=" O LEU 3 112 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA 3 54 " --> pdb=" O GLU 3 106 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '3' and resid 136 through 140 removed outlier: 3.527A pdb=" N SER 3 139 " --> pdb=" O VAL 3 11 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ALA 3 10 " --> pdb=" O ASP 3 25 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL 3 185 " --> pdb=" O LEU 3 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS 3 194 " --> pdb=" O GLU 3 191 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'X' and resid 42 through 45 removed outlier: 3.663A pdb=" N THR X 49 " --> pdb=" O VAL X 45 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER X 48 " --> pdb=" O TYR X 115 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR X 109 " --> pdb=" O SER X 54 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR X 132 " --> pdb=" O TYR X 124 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL X 130 " --> pdb=" O ASP X 126 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'X' and resid 136 through 139 removed outlier: 3.569A pdb=" N THR X 139 " --> pdb=" O VAL X 11 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL X 11 " --> pdb=" O THR X 139 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE X 189 " --> pdb=" O GLU X 200 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '4' and resid 42 through 45 removed outlier: 5.946A pdb=" N SER 4 48 " --> pdb=" O TYR 4 115 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR 4 109 " --> pdb=" O SER 4 54 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL 4 130 " --> pdb=" O ASP 4 126 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '4' and resid 136 through 139 removed outlier: 4.012A pdb=" N VAL 4 11 " --> pdb=" O THR 4 139 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE 4 189 " --> pdb=" O GLU 4 200 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY 4 196 " --> pdb=" O THR 4 193 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Y' and resid 34 through 37 removed outlier: 6.485A pdb=" N LEU Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR Y 44 " --> pdb=" O MET Y 100 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N MET Y 100 " --> pdb=" O THR Y 44 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA Y 46 " --> pdb=" O GLY Y 98 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLY Y 98 " --> pdb=" O ALA Y 46 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN Y 119 " --> pdb=" O ASP Y 115 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Y' and resid 125 through 129 removed outlier: 6.307A pdb=" N THR Y 2 " --> pdb=" O ASP Y 17 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ALA Y 173 " --> pdb=" O SER Y 18 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU Y 176 " --> pdb=" O VAL Y 187 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '5' and resid 34 through 37 removed outlier: 3.555A pdb=" N ILE 5 37 " --> pdb=" O LEU 5 41 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU 5 41 " --> pdb=" O ILE 5 37 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N MET 5 100 " --> pdb=" O THR 5 44 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY 5 98 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN 5 119 " --> pdb=" O ASP 5 115 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '5' and resid 125 through 129 removed outlier: 6.119A pdb=" N THR 5 2 " --> pdb=" O ASP 5 17 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER 5 18 " --> pdb=" O ALA 5 173 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA 5 173 " --> pdb=" O SER 5 18 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU 5 176 " --> pdb=" O VAL 5 187 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Z' and resid 34 through 37 removed outlier: 6.923A pdb=" N ILE Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG Z 40 " --> pdb=" O TRP Z 103 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'Z' and resid 125 through 129 removed outlier: 5.691A pdb=" N THR Z 2 " --> pdb=" O ASP Z 17 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP Z 17 " --> pdb=" O THR Z 2 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER Z 18 " --> pdb=" O VAL Z 173 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL Z 173 " --> pdb=" O SER Z 18 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA Z 178 " --> pdb=" O GLU Z 185 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA Z 180 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '8' and resid 34 through 37 removed outlier: 6.501A pdb=" N ILE 8 41 " --> pdb=" O ILE 8 37 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN 8 40 " --> pdb=" O VAL 8 103 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR 8 42 " --> pdb=" O GLY 8 101 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA 8 97 " --> pdb=" O ALA 8 46 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY 8 102 " --> pdb=" O HIS 8 109 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '8' and resid 124 through 128 removed outlier: 5.853A pdb=" N THR 8 2 " --> pdb=" O ASP 8 17 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN 8 172 " --> pdb=" O THR 8 18 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU 8 175 " --> pdb=" O LEU 8 186 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER 8 179 " --> pdb=" O LYS 8 182 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS 8 182 " --> pdb=" O SER 8 179 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain '7' and resid 34 through 37 removed outlier: 6.711A pdb=" N ILE 7 41 " --> pdb=" O ILE 7 37 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASN 7 40 " --> pdb=" O VAL 7 103 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain '7' and resid 124 through 128 removed outlier: 6.832A pdb=" N THR 7 2 " --> pdb=" O ASP 7 17 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN 7 172 " --> pdb=" O THR 7 18 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU 7 175 " --> pdb=" O LEU 7 186 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER 7 179 " --> pdb=" O LYS 7 182 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS 7 182 " --> pdb=" O SER 7 179 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'G' and resid 65 through 69 removed outlier: 6.416A pdb=" N ARG G 65 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU G 148 " --> pdb=" O TYR G 160 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL G 156 " --> pdb=" O ASP G 152 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'G' and resid 161 through 166 removed outlier: 6.278A pdb=" N TRP G 161 " --> pdb=" O ARG G 40 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR G 35 " --> pdb=" O GLU G 50 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain '6' and resid 34 through 37 removed outlier: 6.649A pdb=" N ILE 6 41 " --> pdb=" O ILE 6 37 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ARG 6 40 " --> pdb=" O TRP 6 103 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain '6' and resid 125 through 129 removed outlier: 5.387A pdb=" N THR 6 2 " --> pdb=" O ASP 6 17 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL 6 173 " --> pdb=" O SER 6 18 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'H' and resid 120 through 123 removed outlier: 6.801A pdb=" N ILE H 112 " --> pdb=" O THR H 99 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N MET H 138 " --> pdb=" O CYS H 98 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY H 141 " --> pdb=" O HIS H 150 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN H 148 " --> pdb=" O ASP H 143 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'H' and resid 236 through 240 removed outlier: 3.940A pdb=" N CYS H 236 " --> pdb=" O ALA H 269 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N CYS H 270 " --> pdb=" O ASN H 314 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY H 216 " --> pdb=" O THR H 321 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG H 339 " --> pdb=" O GLY H 211 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE H 215 " --> pdb=" O ILE H 341 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'I' and resid 130 through 135 removed outlier: 6.813A pdb=" N ASN I 119 " --> pdb=" O ILE I 135 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE I 122 " --> pdb=" O GLU I 113 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS I 148 " --> pdb=" O LEU I 112 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'I' and resid 245 through 250 removed outlier: 3.606A pdb=" N GLY I 226 " --> pdb=" O THR I 331 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG I 349 " --> pdb=" O GLY I 221 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'K' and resid 110 through 114 removed outlier: 6.792A pdb=" N ILE K 102 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA K 128 " --> pdb=" O PHE K 92 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N SER K 129 " --> pdb=" O LEU K 143 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA K 131 " --> pdb=" O ASP K 141 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP K 141 " --> pdb=" O ALA K 131 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'K' and resid 225 through 231 removed outlier: 5.243A pdb=" N LYS K 306 " --> pdb=" O ALA K 260 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE K 262 " --> pdb=" O LYS K 306 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL K 307 " --> pdb=" O ARG K 200 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY K 206 " --> pdb=" O THR K 311 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'L' and resid 55 through 58 removed outlier: 4.987A pdb=" N ARG L 97 " --> pdb=" O LEU L 111 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG L 109 " --> pdb=" O ALA L 99 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'L' and resid 69 through 73 removed outlier: 3.628A pdb=" N ALA L 73 " --> pdb=" O PRO L 77 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'L' and resid 194 through 198 removed outlier: 4.085A pdb=" N ASN L 194 " --> pdb=" O PRO L 227 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY L 174 " --> pdb=" O THR L 279 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'M' and resid 89 through 94 removed outlier: 4.407A pdb=" N ASP M 149 " --> pdb=" O VAL M 93 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU M 150 " --> pdb=" O LEU M 164 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU M 164 " --> pdb=" O LEU M 150 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU M 162 " --> pdb=" O GLY M 152 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'M' and resid 247 through 251 removed outlier: 7.572A pdb=" N LYS M 221 " --> pdb=" O VAL M 326 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL M 328 " --> pdb=" O LYS M 221 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY M 227 " --> pdb=" O THR M 332 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG M 350 " --> pdb=" O GLY M 222 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'J' and resid 78 through 81 removed outlier: 3.595A pdb=" N ARG J 78 " --> pdb=" O LEU J 86 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS J 84 " --> pdb=" O MET J 80 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU J 86 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ARG J 113 " --> pdb=" O LEU J 127 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LYS J 125 " --> pdb=" O ALA J 115 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'J' and resid 209 through 214 removed outlier: 4.943A pdb=" N ASP J 249 " --> pdb=" O VAL J 214 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA J 294 " --> pdb=" O MET J 248 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN J 296 " --> pdb=" O GLU J 250 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY J 190 " --> pdb=" O THR J 295 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'J' and resid 85 through 88 3309 hydrogen bonds defined for protein. 9855 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: 59.88 Time building geometry restraints manager: 92.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 67661 1.06 - 1.28: 11680 1.28 - 1.50: 29376 1.50 - 1.73: 27258 1.73 - 1.95: 666 Bond restraints: 136641 Sorted by residual: bond pdb=" CA ASP B 185 " pdb=" CB ASP B 185 " ideal model delta sigma weight residual 1.530 1.918 -0.388 1.69e-02 3.50e+03 5.27e+02 bond pdb=" CB ASP B 185 " pdb=" CG ASP B 185 " ideal model delta sigma weight residual 1.516 1.948 -0.432 2.50e-02 1.60e+03 2.98e+02 bond pdb=" C GLU B 184 " pdb=" N ASP B 185 " ideal model delta sigma weight residual 1.332 1.529 -0.197 1.40e-02 5.10e+03 1.98e+02 bond pdb=" N ASP B 185 " pdb=" CA ASP B 185 " ideal model delta sigma weight residual 1.457 1.603 -0.146 1.29e-02 6.01e+03 1.28e+02 bond pdb=" CA GLU B 184 " pdb=" C GLU B 184 " ideal model delta sigma weight residual 1.523 1.668 -0.144 1.34e-02 5.57e+03 1.16e+02 ... (remaining 136636 not shown) Histogram of bond angle deviations from ideal: 54.14 - 73.61: 57 73.61 - 93.08: 38 93.08 - 112.55: 161360 112.55 - 132.02: 85616 132.02 - 151.50: 113 Bond angle restraints: 247184 Sorted by residual: angle pdb=" PA ATP H 501 " pdb=" O3A ATP H 501 " pdb=" PB ATP H 501 " ideal model delta sigma weight residual 136.83 116.74 20.09 1.00e+00 1.00e+00 4.04e+02 angle pdb=" HZ2 LYS Q 52 " pdb=" NZ LYS Q 52 " pdb=" HZ3 LYS Q 52 " ideal model delta sigma weight residual 109.00 54.14 54.86 3.00e+00 1.11e-01 3.34e+02 angle pdb=" HZ2 LYS 6 33 " pdb=" NZ LYS 6 33 " pdb=" HZ3 LYS 6 33 " ideal model delta sigma weight residual 109.00 54.16 54.84 3.00e+00 1.11e-01 3.34e+02 angle pdb=" HZ1 LYS L 72 " pdb=" NZ LYS L 72 " pdb=" HZ2 LYS L 72 " ideal model delta sigma weight residual 109.00 54.24 54.76 3.00e+00 1.11e-01 3.33e+02 angle pdb=" HZ1 LYS W 192 " pdb=" NZ LYS W 192 " pdb=" HZ2 LYS W 192 " ideal model delta sigma weight residual 109.00 54.27 54.73 3.00e+00 1.11e-01 3.33e+02 ... (remaining 247179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.13: 52463 25.13 - 50.27: 1439 50.27 - 75.40: 401 75.40 - 100.54: 144 100.54 - 125.67: 1 Dihedral angle restraints: 54448 sinusoidal: 25961 harmonic: 28487 Sorted by residual: dihedral pdb=" CA GLN I 195 " pdb=" C GLN I 195 " pdb=" N GLU I 196 " pdb=" CA GLU I 196 " ideal model delta harmonic sigma weight residual 180.00 115.84 64.16 0 5.00e+00 4.00e-02 1.65e+02 dihedral pdb=" CA GLU J 10 " pdb=" C GLU J 10 " pdb=" N LEU J 11 " pdb=" CA LEU J 11 " ideal model delta harmonic sigma weight residual 180.00 134.46 45.54 0 5.00e+00 4.00e-02 8.30e+01 dihedral pdb=" CA TRP T 215 " pdb=" C TRP T 215 " pdb=" N VAL T 216 " pdb=" CA VAL T 216 " ideal model delta harmonic sigma weight residual 180.00 139.01 40.99 0 5.00e+00 4.00e-02 6.72e+01 ... (remaining 54445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 10146 0.112 - 0.223: 295 0.223 - 0.335: 2 0.335 - 0.447: 0 0.447 - 0.558: 1 Chirality restraints: 10444 Sorted by residual: chirality pdb=" CA ASP B 185 " pdb=" N ASP B 185 " pdb=" C ASP B 185 " pdb=" CB ASP B 185 " both_signs ideal model delta sigma weight residual False 2.51 3.07 -0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" CA GLN I 195 " pdb=" N GLN I 195 " pdb=" C GLN I 195 " pdb=" CB GLN I 195 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA GLU B 184 " pdb=" N GLU B 184 " pdb=" C GLU B 184 " pdb=" CB GLU B 184 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 10441 not shown) Planarity restraints: 20310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 186 " 0.024 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C ALA B 186 " -0.086 2.00e-02 2.50e+03 pdb=" O ALA B 186 " 0.033 2.00e-02 2.50e+03 pdb=" N ILE B 187 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 153 " 0.073 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO H 154 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO H 154 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO H 154 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN Y 38 " 0.064 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO Y 39 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO Y 39 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO Y 39 " 0.052 5.00e-02 4.00e+02 ... (remaining 20307 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 2872 2.09 - 2.72: 235809 2.72 - 3.35: 378301 3.35 - 3.97: 516038 3.97 - 4.60: 812173 Nonbonded interactions: 1945193 Sorted by model distance: nonbonded pdb=" H GLY C 158 " pdb=" HG1 THR D 58 " model vdw 1.463 2.100 nonbonded pdb=" O LYS K 70 " pdb=" H LEU K 73 " model vdw 1.503 1.850 nonbonded pdb=" HG1 THR Q 31 " pdb=" O ARG Q 163 " model vdw 1.525 1.850 nonbonded pdb=" OE1 GLU J 218 " pdb=" H GLU J 218 " model vdw 1.526 1.850 nonbonded pdb=" OE1 GLU H 371 " pdb=" H GLU H 371 " model vdw 1.534 1.850 ... (remaining 1945188 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 'U' } ncs_group { reference = chain '2' selection = chain 'V' } ncs_group { reference = chain '3' selection = chain 'W' } ncs_group { reference = chain '4' selection = chain 'X' } ncs_group { reference = chain '5' selection = chain 'Y' } ncs_group { reference = chain '6' selection = (chain 'Z' and resid 1 through 199) } ncs_group { reference = chain '7' selection = chain '8' } ncs_group { reference = chain 'A' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'P' } ncs_group { reference = chain 'D' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'S' } ncs_group { reference = chain 'G' selection = (chain 'T' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 6 through 245)) } 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: 7 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 399 5.16 5 C 42652 2.51 5 N 11666 2.21 5 O 12953 1.98 5 H 67796 0.53 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: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.480 Extract box with map and model: 20.270 Check model and map are aligned: 1.490 Convert atoms to be neutral: 0.860 Process input model: 350.940 Find NCS groups from input model: 5.520 Set up NCS constraints: 0.690 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 387.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 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 : 0.007 0.432 68845 Z= 0.470 Angle : 0.962 29.956 92967 Z= 0.552 Chirality : 0.047 0.558 10444 Planarity : 0.006 0.102 12017 Dihedral : 15.497 125.673 25929 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 1.95 % Allowed : 9.58 % Favored : 88.47 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.01 (0.07), residues: 8569 helix: -3.86 (0.05), residues: 3267 sheet: -2.16 (0.11), residues: 1690 loop : -3.21 (0.08), residues: 3612 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 223 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Evaluate side-chains 4040 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 3822 time to evaluate : 7.976 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 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 218 outliers final: 90 residues processed: 3921 average time/residue: 1.7562 time to fit residues: 11262.1866 Evaluate side-chains 2828 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 2738 time to evaluate : 8.019 Switching outliers to nearest non-outliers revert: symmetry clash 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: 90 outliers final: 9 residues processed: 90 average time/residue: 1.5216 time to fit residues: 248.4704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 717 optimal weight: 3.9990 chunk 644 optimal weight: 0.8980 chunk 357 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 434 optimal weight: 0.8980 chunk 344 optimal weight: 1.9990 chunk 666 optimal weight: 0.6980 chunk 257 optimal weight: 2.9990 chunk 405 optimal weight: 3.9990 chunk 495 optimal weight: 2.9990 chunk 771 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN ** N 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 GLN ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 88 ASN P 123 GLN ** R 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN S 121 GLN S 190 HIS U 36 HIS V 55 GLN V 63 ASN V 71 ASN ** W 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 108 ASN Y 70 ASN Z 53 GLN 8 193 ASN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN C 95 GLN C 240 HIS D 54 GLN F 152 ASN F 166 GLN F 185 ASN 1 80 ASN ** 1 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 160 ASN 2 27 GLN 2 63 ASN 4 69 GLN 5 89 GLN 6 7 GLN 6 110 GLN H 117 GLN H 305 GLN H 379 ASN I 81 ASN I 84 GLN ** I 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 GLN ** K 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 262 ASN M 395 GLN J 67 GLN J 288 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 68845 Z= 0.293 Angle : 0.758 9.199 92967 Z= 0.410 Chirality : 0.045 0.276 10444 Planarity : 0.006 0.114 12017 Dihedral : 6.596 122.608 9496 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.10 % Favored : 94.52 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.08), residues: 8569 helix: -1.66 (0.08), residues: 3340 sheet: -1.41 (0.11), residues: 1702 loop : -2.55 (0.09), residues: 3527 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 223 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Evaluate side-chains 3150 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 2914 time to evaluate : 8.220 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 236 outliers final: 170 residues processed: 3015 average time/residue: 1.6668 time to fit residues: 8373.6493 Evaluate side-chains 2756 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 2586 time to evaluate : 7.708 Switching outliers to nearest non-outliers 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: 170 outliers final: 8 residues processed: 170 average time/residue: 1.3328 time to fit residues: 424.5476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 428 optimal weight: 0.9980 chunk 239 optimal weight: 0.9990 chunk 642 optimal weight: 3.9990 chunk 525 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 773 optimal weight: 0.7980 chunk 835 optimal weight: 3.9990 chunk 688 optimal weight: 4.9990 chunk 766 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 620 optimal weight: 0.0980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN ** N 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 GLN ** R 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 214 ASN S 65 HIS T 105 ASN T 170 GLN U 160 ASN ** W 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 119 ASN Z 123 GLN A 193 GLN B 165 ASN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN F 21 GLN F 203 GLN G 170 GLN ** 1 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 160 ASN 2 27 GLN 6 66 HIS H 305 GLN I 314 ASN K 137 ASN K 175 GLN K 193 GLN K 376 ASN K 380 GLN ** L 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 68845 Z= 0.230 Angle : 0.651 9.137 92967 Z= 0.348 Chirality : 0.043 0.249 10444 Planarity : 0.005 0.110 12017 Dihedral : 6.030 109.668 9496 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.19 % Favored : 94.50 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.05 % 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: -2.13 (0.08), residues: 8569 helix: -0.66 (0.08), residues: 3386 sheet: -1.13 (0.12), residues: 1690 loop : -2.24 (0.09), residues: 3493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 223 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Evaluate side-chains 2844 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 2712 time to evaluate : 7.987 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 83 residues processed: 2757 average time/residue: 1.6756 time to fit residues: 7737.3082 Evaluate side-chains 2585 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 2502 time to evaluate : 8.067 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 7 residues processed: 83 average time/residue: 1.3891 time to fit residues: 219.5398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 764 optimal weight: 0.8980 chunk 581 optimal weight: 0.9990 chunk 401 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 369 optimal weight: 0.6980 chunk 519 optimal weight: 0.3980 chunk 776 optimal weight: 2.9990 chunk 821 optimal weight: 3.9990 chunk 405 optimal weight: 2.9990 chunk 735 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 121 GLN U 160 ASN ** W 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 3 ASN Z 123 GLN A 150 GLN B 165 ASN C 146 GLN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN E 13 ASN ** 1 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 160 ASN 2 61 GLN 3 31 GLN H 117 GLN K 193 GLN K 376 ASN ** L 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 ASN J 270 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 68845 Z= 0.224 Angle : 0.624 10.617 92967 Z= 0.331 Chirality : 0.042 0.245 10444 Planarity : 0.005 0.109 12017 Dihedral : 5.715 96.813 9496 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.50 % Favored : 95.20 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.09), residues: 8569 helix: -0.07 (0.09), residues: 3399 sheet: -1.00 (0.12), residues: 1684 loop : -1.93 (0.10), residues: 3486 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 223 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Evaluate side-chains 2747 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 2605 time to evaluate : 7.221 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 142 outliers final: 107 residues processed: 2657 average time/residue: 1.6234 time to fit residues: 7215.5947 Evaluate side-chains 2612 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 2505 time to evaluate : 7.908 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 7 residues processed: 107 average time/residue: 1.2695 time to fit residues: 263.2440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 684 optimal weight: 0.8980 chunk 466 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 611 optimal weight: 3.9990 chunk 339 optimal weight: 0.0670 chunk 701 optimal weight: 3.9990 chunk 567 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 419 optimal weight: 0.9980 chunk 737 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 95 GLN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 186 HIS R 204 GLN U 160 ASN ** W 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 66 HIS ** 8 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN G 68 ASN ** 1 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 160 ASN 3 31 GLN 3 33 GLN 4 104 ASN ** 5 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 ASN I 131 HIS ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 68845 Z= 0.238 Angle : 0.605 8.541 92967 Z= 0.321 Chirality : 0.042 0.250 10444 Planarity : 0.005 0.109 12017 Dihedral : 5.488 85.246 9496 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.92 % Favored : 94.78 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.05 % 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: -1.16 (0.09), residues: 8569 helix: 0.30 (0.09), residues: 3404 sheet: -0.86 (0.12), residues: 1683 loop : -1.74 (0.10), residues: 3482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 223 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Evaluate side-chains 2684 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 2576 time to evaluate : 8.027 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 revert: symmetry clash outliers start: 108 outliers final: 77 residues processed: 2607 average time/residue: 1.6572 time to fit residues: 7228.7542 Evaluate side-chains 2573 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 2496 time to evaluate : 8.125 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 5 residues processed: 77 average time/residue: 1.3478 time to fit residues: 200.8039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 276 optimal weight: 1.9990 chunk 739 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 482 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 822 optimal weight: 0.3980 chunk 682 optimal weight: 2.9990 chunk 380 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 272 optimal weight: 0.8980 chunk 431 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 160 ASN W 40 GLN ** W 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN B 165 ASN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN ** 1 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 160 ASN 3 31 GLN 4 108 ASN ** 5 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 119 ASN 7 62 ASN I 119 ASN ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 68845 Z= 0.302 Angle : 0.616 8.301 92967 Z= 0.329 Chirality : 0.042 0.293 10444 Planarity : 0.005 0.109 12017 Dihedral : 5.404 78.150 9496 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.22 % Favored : 94.54 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.05 % 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: -1.02 (0.09), residues: 8569 helix: 0.46 (0.09), residues: 3401 sheet: -0.81 (0.12), residues: 1699 loop : -1.71 (0.10), residues: 3469 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 223 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Evaluate side-chains 2636 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 2505 time to evaluate : 9.336 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 outliers start: 131 outliers final: 102 residues processed: 2544 average time/residue: 1.5869 time to fit residues: 6743.7455 Evaluate side-chains 2525 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 2423 time to evaluate : 8.061 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 4 residues processed: 102 average time/residue: 1.2975 time to fit residues: 256.5266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 792 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 468 optimal weight: 2.9990 chunk 600 optimal weight: 2.9990 chunk 465 optimal weight: 0.5980 chunk 692 optimal weight: 3.9990 chunk 459 optimal weight: 2.9990 chunk 819 optimal weight: 2.9990 chunk 512 optimal weight: 0.8980 chunk 499 optimal weight: 2.9990 chunk 378 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 24 GLN ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 ASN U 160 ASN ** W 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 193 ASN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS E 13 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 160 ASN 2 132 HIS I 119 ASN ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 68845 Z= 0.364 Angle : 0.641 8.540 92967 Z= 0.343 Chirality : 0.043 0.315 10444 Planarity : 0.005 0.117 12017 Dihedral : 5.397 74.282 9496 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.07 % Favored : 93.70 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -0.99 (0.09), residues: 8569 helix: 0.53 (0.09), residues: 3398 sheet: -0.82 (0.12), residues: 1696 loop : -1.72 (0.10), residues: 3475 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 223 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Evaluate side-chains 2573 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 2460 time to evaluate : 8.049 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 outliers start: 113 outliers final: 89 residues processed: 2498 average time/residue: 1.5983 time to fit residues: 6654.8383 Evaluate side-chains 2499 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 2410 time to evaluate : 8.018 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 2 residues processed: 89 average time/residue: 1.1973 time to fit residues: 207.7945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 506 optimal weight: 0.5980 chunk 327 optimal weight: 3.9990 chunk 489 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 520 optimal weight: 0.6980 chunk 558 optimal weight: 0.9990 chunk 405 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 643 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 95 GLN P 123 GLN ** R 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 160 ASN V 55 GLN ** W 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 24 GLN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 160 ASN 2 132 HIS 3 33 GLN 5 29 GLN 7 62 ASN H 47 GLN I 119 ASN K 376 ASN L 124 HIS ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.131 68845 Z= 0.200 Angle : 0.595 9.534 92967 Z= 0.313 Chirality : 0.042 0.310 10444 Planarity : 0.005 0.115 12017 Dihedral : 5.251 72.955 9496 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.57 % Favored : 95.18 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.05 % 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: -0.64 (0.09), residues: 8569 helix: 0.82 (0.09), residues: 3382 sheet: -0.68 (0.12), residues: 1669 loop : -1.50 (0.10), residues: 3518 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 223 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Evaluate side-chains 2596 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 2536 time to evaluate : 7.963 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 outliers start: 60 outliers final: 48 residues processed: 2552 average time/residue: 1.5864 time to fit residues: 6749.2815 Evaluate side-chains 2492 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 2444 time to evaluate : 7.950 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 48 outliers final: 1 residues processed: 48 average time/residue: 1.2435 time to fit residues: 119.0379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 745 optimal weight: 2.9990 chunk 784 optimal weight: 0.9980 chunk 716 optimal weight: 2.9990 chunk 763 optimal weight: 3.9990 chunk 459 optimal weight: 2.9990 chunk 332 optimal weight: 0.7980 chunk 599 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 689 optimal weight: 5.9990 chunk 722 optimal weight: 2.9990 chunk 760 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 160 ASN ** W 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN E 152 GLN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 160 ASN ** 3 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 175 ASN I 57 GLN ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 395 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.093 68845 Z= 0.293 Angle : 0.616 10.162 92967 Z= 0.328 Chirality : 0.042 0.380 10444 Planarity : 0.005 0.115 12017 Dihedral : 5.197 72.914 9496 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.76 % Favored : 94.04 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -0.65 (0.09), residues: 8569 helix: 0.82 (0.09), residues: 3393 sheet: -0.71 (0.12), residues: 1687 loop : -1.50 (0.10), residues: 3489 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 223 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Evaluate side-chains 2540 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 2467 time to evaluate : 8.055 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 outliers start: 73 outliers final: 60 residues processed: 2481 average time/residue: 1.5784 time to fit residues: 6523.4752 Evaluate side-chains 2494 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 2434 time to evaluate : 8.024 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 60 outliers final: 1 residues processed: 60 average time/residue: 1.2262 time to fit residues: 148.9064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 501 optimal weight: 0.9980 chunk 807 optimal weight: 3.9990 chunk 492 optimal weight: 1.9990 chunk 382 optimal weight: 0.5980 chunk 561 optimal weight: 1.9990 chunk 846 optimal weight: 0.9990 chunk 779 optimal weight: 3.9990 chunk 674 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 520 optimal weight: 1.9990 chunk 413 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 204 GLN ** S 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 160 ASN ** W 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 47 ASN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 GLN E 13 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 160 ASN ** 3 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 175 ASN H 47 GLN ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 288 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.115 68845 Z= 0.226 Angle : 0.612 10.590 92967 Z= 0.322 Chirality : 0.042 0.323 10444 Planarity : 0.005 0.114 12017 Dihedral : 5.156 71.884 9496 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.85 % Favored : 94.95 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -0.50 (0.09), residues: 8569 helix: 0.94 (0.09), residues: 3399 sheet: -0.69 (0.12), residues: 1700 loop : -1.40 (0.10), residues: 3470 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17138 Ramachandran restraints generated. 8569 Oldfield, 0 Emsley, 8569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 223 is missing expected H atoms. Skipping. Residue THR 233 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Evaluate side-chains 2517 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 2493 time to evaluate : 7.237 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: 24 outliers final: 22 residues processed: 2500 average time/residue: 1.5738 time to fit residues: 6570.1132 Evaluate side-chains 2446 residues out of total 7270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 2424 time to evaluate : 7.979 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 1.3257 time to fit residues: 63.0371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 535 optimal weight: 2.9990 chunk 718 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 621 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 675 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 693 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 94 GLN ** P 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 152 GLN R 204 GLN ** S 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 160 ASN ** W 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN B 94 GLN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 160 ASN 3 81 GLN ** 3 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 175 ASN ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 288 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.089804 restraints weight = 338438.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.094057 restraints weight = 139118.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.096731 restraints weight = 75659.216| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.109 68845 Z= 0.335 Angle : 0.637 10.340 92967 Z= 0.339 Chirality : 0.042 0.313 10444 Planarity : 0.005 0.113 12017 Dihedral : 5.166 72.196 9496 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.58 % Favored : 93.24 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -0.63 (0.09), residues: 8569 helix: 0.86 (0.09), residues: 3393 sheet: -0.73 (0.12), residues: 1690 loop : -1.51 (0.10), residues: 3486 =============================================================================== Job complete usr+sys time: 85560.97 seconds wall clock time: 1437 minutes 56.16 seconds (86276.16 seconds total)