Starting phenix.real_space_refine (version: dev) on Wed May 25 06:45:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohx_12912/05_2022/7ohx_12912.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohx_12912/05_2022/7ohx_12912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohx_12912/05_2022/7ohx_12912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohx_12912/05_2022/7ohx_12912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohx_12912/05_2022/7ohx_12912.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohx_12912/05_2022/7ohx_12912.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "3 GLU 4": "OE1" <-> "OE2" Residue "3 TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 ASP 56": "OD1" <-> "OD2" Residue "3 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 GLU 68": "OE1" <-> "OE2" Residue "3 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 GLU 122": "OE1" <-> "OE2" Residue "3 ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 GLU 165": "OE1" <-> "OE2" Residue "4 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 GLU 36": "OE1" <-> "OE2" Residue "4 PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 68": "OE1" <-> "OE2" Residue "4 ASP 78": "OD1" <-> "OD2" Residue "4 ASP 114": "OD1" <-> "OD2" Residue "4 ASP 147": "OD1" <-> "OD2" Residue "4 ASP 179": "OD1" <-> "OD2" Residue "4 ASP 216": "OD1" <-> "OD2" Residue "4 TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 GLU 236": "OE1" <-> "OE2" Residue "4 GLU 240": "OE1" <-> "OE2" Residue "4 ASP 241": "OD1" <-> "OD2" Residue "5 PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 GLU 55": "OE1" <-> "OE2" Residue "5 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 ASP 104": "OD1" <-> "OD2" Residue "5 PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 GLU 210": "OE1" <-> "OE2" Residue "5 ASP 220": "OD1" <-> "OD2" Residue "5 ASP 241": "OD1" <-> "OD2" Residue "5 ARG 252": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 GLU 262": "OE1" <-> "OE2" Residue "5 TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 ARG 300": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 ASP 359": "OD1" <-> "OD2" Residue "5 ARG 382": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 ASP 411": "OD1" <-> "OD2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 216": "OD1" <-> "OD2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 375": "OE1" <-> "OE2" Residue "C ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C ARG 326": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 71": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 177": "OD1" <-> "OD2" Residue "D ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ARG 286": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D ARG 340": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 376": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 14": "OD1" <-> "OD2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 182": "OD1" <-> "OD2" Residue "F PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 112": "OE1" <-> "OE2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 158": "OD1" <-> "OD2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "G ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 153": "OD1" <-> "OD2" Residue "H ARG 173": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 189": "OE1" <-> "OE2" Residue "K ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 35": "OE1" <-> "OE2" Residue "K PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "K ASP 152": "OD1" <-> "OD2" Residue "K ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 183": "OD1" <-> "OD2" Residue "K GLU 203": "OE1" <-> "OE2" Residue "K TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 240": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 257": "OE1" <-> "OE2" Residue "K GLU 258": "OE1" <-> "OE2" Residue "K ASP 261": "OD1" <-> "OD2" Residue "K GLU 264": "OE1" <-> "OE2" Residue "K ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 285": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 40": "OD1" <-> "OD2" Residue "M PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 8": "OE1" <-> "OE2" Residue "N ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N ASP 124": "OD1" <-> "OD2" Residue "N PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 145": "OD1" <-> "OD2" Residue "O GLU 40": "OE1" <-> "OE2" Residue "O PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 100": "OE1" <-> "OE2" Residue "O TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 187": "OE1" <-> "OE2" Residue "P ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ASP 108": "OD1" <-> "OD2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "Q TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "S PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 21": "OE1" <-> "OE2" Residue "S PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 34": "OE1" <-> "OE2" Residue "S TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 24": "OE1" <-> "OE2" Residue "W ARG 31": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ASP 35": "OD1" <-> "OD2" Residue "W TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ASP 108": "OD1" <-> "OD2" Residue "W PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ASP 224": "OD1" <-> "OD2" Residue "Y TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ASP 53": "OD1" <-> "OD2" Residue "Y GLU 67": "OE1" <-> "OE2" Residue "Y PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ASP 164": "OD1" <-> "OD2" Residue "b TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 210": "OD1" <-> "OD2" Residue "b GLU 325": "OE1" <-> "OE2" Residue "b ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 423": "OE1" <-> "OE2" Residue "b TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 464": "OE1" <-> "OE2" Residue "b GLU 466": "OE1" <-> "OE2" Residue "b PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f GLU 33": "OE1" <-> "OE2" Residue "f TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h GLU 8": "OE1" <-> "OE2" Residue "h ASP 79": "OD1" <-> "OD2" Residue "h ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m GLU 251": "OE1" <-> "OE2" Residue "m PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m GLU 272": "OE1" <-> "OE2" Residue "m GLU 342": "OE1" <-> "OE2" Residue "m GLU 355": "OE1" <-> "OE2" Residue "n ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n GLU 107": "OE1" <-> "OE2" Residue "n ASP 131": "OD1" <-> "OD2" Residue "n ARG 174": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ASP 214": "OD1" <-> "OD2" Residue "n PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n GLU 223": "OE1" <-> "OE2" Residue "n TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ASP 413": "OD1" <-> "OD2" Residue "n ARG 414": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 424": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n GLU 451": "OE1" <-> "OE2" Residue "o TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o ARG 207": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ASP 83": "OD1" <-> "OD2" Residue "t ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t GLU 226": "OE1" <-> "OE2" Residue "t ASP 241": "OD1" <-> "OD2" Residue "u ARG 2": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "u ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u GLU 28": "OE1" <-> "OE2" Residue "u ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u GLU 62": "OE1" <-> "OE2" Residue "u ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u GLU 84": "OE1" <-> "OE2" Residue "u GLU 104": "OE1" <-> "OE2" Residue "u ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "v ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "v TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v ASP 202": "OD1" <-> "OD2" Residue "v TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x GLU 25": "OE1" <-> "OE2" Residue "x ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "x ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "x TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x GLU 116": "OE1" <-> "OE2" Residue "x TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x ASP 146": "OD1" <-> "OD2" Residue "x PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x GLU 196": "OE1" <-> "OE2" Residue "x GLU 225": "OE1" <-> "OE2" Residue "x PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x ARG 272": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "x GLU 285": "OE1" <-> "OE2" Residue "x GLU 289": "OE1" <-> "OE2" Residue "x TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "y PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "y ARG 85": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "y ASP 90": "OD1" <-> "OD2" Residue "y GLU 99": "OE1" <-> "OE2" Residue "y ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "y GLU 126": "OE1" <-> "OE2" Residue "y TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 157028 Number of models: 1 Model: "" Number of chains: 39 Chain: "1" Number of atoms: 50227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1561, 50227 Classifications: {'RNA': 1561} Modifications used: {'rna3p_pyr': 579, 'rna2p_pur': 158, 'rna3p_pur': 719, 'rna2p_pyr': 105, '3*END': 1} Link IDs: {'rna3p': 1298, 'rna2p': 262} Chain breaks: 39 Chain: "2" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 4736 Classifications: {'RNA': 148} Modifications used: {'rna3p_pyr': 61, 'rna2p_pur': 14, 'rna3p_pur': 61, 'rna2p_pyr': 12} Link IDs: {'rna3p': 122, 'rna2p': 25} Chain breaks: 3 Chain: "3" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2908 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 5, 'TRANS': 167} Chain: "4" Number of atoms: 3744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3744 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain breaks: 3 Chain: "5" Number of atoms: 6170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 6170 Classifications: {'peptide': 385} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 372, 'PCIS': 1} Chain breaks: 3 Chain: "6" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 2061 Classifications: {'RNA': 65} Modifications used: {'rna3p_pyr': 18, 'rna2p_pur': 8, 'rna3p_pur': 21, 'rna2p_pyr': 18, '3*END': 1} Link IDs: {'rna3p': 39, 'rna2p': 25} Chain breaks: 1 Chain: "B" Number of atoms: 5093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5093 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 10, 'TRANS': 304} Chain breaks: 1 Chain: "C" Number of atoms: 5336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5336 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 15, 'TRANS': 326, 'PCIS': 1} Chain: "D" Number of atoms: 6897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6897 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 20, 'TRANS': 403} Chain breaks: 3 Chain: "E" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 2497 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 143, 'PCIS': 1} Chain breaks: 1 Chain: "F" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3969 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "G" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 2345 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain breaks: 2 Chain: "H" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2008 Classifications: {'peptide': 123} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 122} Chain breaks: 4 Chain: "K" Number of atoms: 3956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3956 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 9, 'TRANS': 229} Chain breaks: 2 Chain: "L" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1782 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2179 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "N" Number of atoms: 3079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3079 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "O" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 3080 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 7, 'TRANS': 179, 'PCIS': 1} Chain breaks: 1 Chain: "P" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2014 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 3 Chain: "Q" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2101 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "S" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2904 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "W" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2075 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 7 Chain: "Y" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2060 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "b" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 4030 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 9, 'TRANS': 238} Chain breaks: 8 Chain: "e" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2057 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "f" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1731 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 101, 'PCIS': 1} Chain: "h" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Chain: "i" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 413 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "j" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1137 Classifications: {'peptide': 71} Link IDs: {'TRANS': 69, 'PCIS': 1} Chain: "m" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1790 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 12, 'TRANS': 93} Chain breaks: 3 Chain: "n" Number of atoms: 4111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 4111 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 11, 'TRANS': 231} Chain breaks: 12 Chain: "o" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1901 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "t" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3287 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 7, 'TRANS': 193, 'PCIS': 1} Chain breaks: 6 Chain: "u" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1729 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Chain: "v" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2223 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain breaks: 2 Chain: "x" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 4573 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 12, 'TRANS': 254} Chain breaks: 2 Chain: "y" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2854 Classifications: {'peptide': 189} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain breaks: 3 Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0PU8 SG CYS j 19 144.826 94.410 134.368 1.00109.48 S ATOM A0PVL SG CYS j 22 141.760 94.676 132.119 1.00 87.45 S ATOM A0Q1A SG CYS j 34 143.349 97.832 133.608 1.00 98.44 S ATOM A0Q27 SG CYS j 37 141.466 95.430 135.828 1.00 75.92 S ATOM A0ZAX SG CYS u 6 186.903 148.386 51.756 1.00170.73 S ATOM A0ZC9 SG CYS u 9 187.483 145.390 50.881 1.00221.58 S ATOM A0ZM6 SG CYS u 32 183.575 145.494 50.822 1.00299.18 S Residues with excluded nonbonded symmetry interactions: 189 residue: pdb=" N ASP 4 57 " occ=0.52 ... (10 atoms not shown) pdb=" HB3 ASP 4 57 " occ=0.52 residue: pdb=" N VAL O 3 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (13 atoms not shown) pdb=" HG3 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (12 atoms not shown) pdb=" HD3 PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (17 atoms not shown) pdb="HD13 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (10 atoms not shown) pdb=" HB3 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (5 atoms not shown) pdb=" HA3 GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (20 atoms not shown) pdb=" HZ3 LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (5 atoms not shown) pdb=" HA3 GLY O 13 " occ=0.50 ... (remaining 177 not shown) Time building chain proxies: 55.70, per 1000 atoms: 0.35 Number of scatterers: 157028 At special positions: 0 Unit cell: (219.081, 255.24, 285.018, 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) Zn 2 29.99 S 123 16.00 P 1774 15.00 O 21063 8.00 N 15763 7.00 C 48264 6.00 H 70039 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: 105.35 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " pdb=" ZN u 201 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 9 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 6 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 32 " Number of angles added : 6 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11544 Finding SS restraints... Secondary structure from input PDB file: 252 helices and 66 sheets defined 44.5% alpha, 15.2% beta 531 base pairs and 786 stacking pairs defined. Time for finding SS restraints: 55.78 Creating SS restraints... Processing helix chain '3' and resid 2 through 13 Processing helix chain '3' and resid 43 through 47 removed outlier: 3.541A pdb=" N ASN 3 47 " --> pdb=" O PRO 3 44 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 70 Processing helix chain '3' and resid 72 through 76 Processing helix chain '3' and resid 85 through 97 Processing helix chain '3' and resid 101 through 118 Processing helix chain '3' and resid 119 through 127 Processing helix chain '3' and resid 138 through 157 removed outlier: 3.727A pdb=" N LYS 3 157 " --> pdb=" O LEU 3 153 " (cutoff:3.500A) Processing helix chain '3' and resid 157 through 171 Processing helix chain '4' and resid 6 through 11 Processing helix chain '4' and resid 14 through 29 removed outlier: 4.090A pdb=" N LYS 4 27 " --> pdb=" O GLU 4 23 " (cutoff:3.500A) Processing helix chain '4' and resid 31 through 36 removed outlier: 3.621A pdb=" N LYS 4 35 " --> pdb=" O ALA 4 31 " (cutoff:3.500A) Processing helix chain '4' and resid 38 through 55 removed outlier: 4.074A pdb=" N PHE 4 42 " --> pdb=" O LYS 4 38 " (cutoff:3.500A) Processing helix chain '4' and resid 58 through 76 removed outlier: 4.154A pdb=" N HIS 4 73 " --> pdb=" O LEU 4 69 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY 4 74 " --> pdb=" O GLY 4 70 " (cutoff:3.500A) Processing helix chain '4' and resid 91 through 109 removed outlier: 4.013A pdb=" N PHE 4 95 " --> pdb=" O ASN 4 91 " (cutoff:3.500A) Processing helix chain '4' and resid 117 through 132 Processing helix chain '4' and resid 142 through 155 removed outlier: 4.007A pdb=" N ARG 4 155 " --> pdb=" O LYS 4 151 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 182 removed outlier: 4.777A pdb=" N LEU 4 178 " --> pdb=" O VAL 4 174 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP 4 179 " --> pdb=" O ASP 4 175 " (cutoff:3.500A) Processing helix chain '4' and resid 183 through 185 No H-bonds generated for 'chain '4' and resid 183 through 185' Processing helix chain '4' and resid 213 through 214 No H-bonds generated for 'chain '4' and resid 213 through 214' Processing helix chain '4' and resid 216 through 218 No H-bonds generated for 'chain '4' and resid 216 through 218' Processing helix chain '4' and resid 221 through 227 Processing helix chain '4' and resid 231 through 242 Processing helix chain '5' and resid 42 through 45 Processing helix chain '5' and resid 119 through 126 removed outlier: 4.451A pdb=" N LEU 5 123 " --> pdb=" O ASP 5 119 " (cutoff:3.500A) Processing helix chain '5' and resid 297 through 301 removed outlier: 3.751A pdb=" N ARG 5 300 " --> pdb=" O LEU 5 297 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU 5 301 " --> pdb=" O PRO 5 298 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 297 through 301' Processing helix chain 'B' and resid 111 through 117 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 141 through 154 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 381 removed outlier: 3.979A pdb=" N HIS B 377 " --> pdb=" O PRO B 373 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 removed outlier: 3.851A pdb=" N LYS C 44 " --> pdb=" O THR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 129 removed outlier: 3.519A pdb=" N THR C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 181 Processing helix chain 'C' and resid 190 through 195 removed outlier: 3.547A pdb=" N TYR C 194 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 221 removed outlier: 4.427A pdb=" N ASN C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 252 through 263 removed outlier: 4.001A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 removed outlier: 4.140A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 Processing helix chain 'C' and resid 320 through 328 removed outlier: 3.608A pdb=" N LEU C 324 " --> pdb=" O ASN C 320 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.493A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU C 337 " --> pdb=" O VAL C 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 47 Processing helix chain 'D' and resid 50 through 61 Processing helix chain 'D' and resid 66 through 78 Proline residue: D 74 - end of helix Processing helix chain 'D' and resid 91 through 108 Proline residue: D 99 - end of helix Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.743A pdb=" N GLY D 114 " --> pdb=" O PRO D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 139 removed outlier: 3.771A pdb=" N LEU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 162 removed outlier: 3.616A pdb=" N MET D 162 " --> pdb=" O ALA D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 182 removed outlier: 3.859A pdb=" N LEU D 176 " --> pdb=" O PRO D 172 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'D' and resid 206 through 217 removed outlier: 3.673A pdb=" N GLN D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 243 Processing helix chain 'D' and resid 275 through 287 Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 324 through 339 removed outlier: 3.512A pdb=" N PHE D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 352 Processing helix chain 'D' and resid 369 through 384 Processing helix chain 'D' and resid 395 through 400 removed outlier: 4.022A pdb=" N LEU D 399 " --> pdb=" O PRO D 396 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY D 400 " --> pdb=" O ASN D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 408 Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.623A pdb=" N LEU D 432 " --> pdb=" O GLN D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 456 Processing helix chain 'D' and resid 464 through 468 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 92 through 96 removed outlier: 4.096A pdb=" N GLY E 95 " --> pdb=" O SER E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.864A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'F' and resid 9 through 72 removed outlier: 3.593A pdb=" N GLN F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 120 through 130 removed outlier: 4.018A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.633A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 222 through 226 Processing helix chain 'F' and resid 234 through 244 removed outlier: 4.532A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 97 removed outlier: 3.691A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 117 Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 160 through 165 removed outlier: 4.523A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 182 through 189 removed outlier: 4.007A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 223 Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.501A pdb=" N ALA H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 163 Processing helix chain 'K' and resid 33 through 48 removed outlier: 3.929A pdb=" N VAL K 37 " --> pdb=" O PRO K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 77 Processing helix chain 'K' and resid 106 through 114 removed outlier: 3.714A pdb=" N TRP K 110 " --> pdb=" O PHE K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 117 No H-bonds generated for 'chain 'K' and resid 115 through 117' Processing helix chain 'K' and resid 128 through 134 Processing helix chain 'K' and resid 139 through 143 removed outlier: 4.185A pdb=" N GLN K 143 " --> pdb=" O ASP K 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 139 through 143' Processing helix chain 'K' and resid 144 through 148 Processing helix chain 'K' and resid 157 through 163 removed outlier: 3.656A pdb=" N LYS K 161 " --> pdb=" O GLY K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 175 Processing helix chain 'K' and resid 184 through 188 removed outlier: 4.543A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 184 through 188' Processing helix chain 'K' and resid 190 through 195 Processing helix chain 'K' and resid 196 through 201 removed outlier: 3.969A pdb=" N LYS K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 232 Processing helix chain 'K' and resid 255 through 274 removed outlier: 4.249A pdb=" N ASP K 261 " --> pdb=" O GLU K 257 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 83 Processing helix chain 'L' and resid 86 through 93 removed outlier: 3.680A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 97 Processing helix chain 'M' and resid 97 through 111 Processing helix chain 'M' and resid 113 through 135 removed outlier: 3.531A pdb=" N THR M 130 " --> pdb=" O GLN M 126 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS M 133 " --> pdb=" O TYR M 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.764A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 32 removed outlier: 3.822A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'N' and resid 177 through 184 removed outlier: 5.796A pdb=" N ASN N 182 " --> pdb=" O LYS N 179 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS N 184 " --> pdb=" O ASN N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 196 removed outlier: 3.595A pdb=" N THR N 190 " --> pdb=" O GLY N 186 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TRP N 191 " --> pdb=" O ARG N 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 29 removed outlier: 3.691A pdb=" N ASN O 29 " --> pdb=" O LYS O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 54 through 59 Processing helix chain 'O' and resid 75 through 87 removed outlier: 3.661A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 100 Processing helix chain 'O' and resid 111 through 115 Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 145 Processing helix chain 'O' and resid 149 through 162 Processing helix chain 'O' and resid 163 through 186 Processing helix chain 'O' and resid 188 through 197 Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 70 through 75 removed outlier: 3.982A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'Q' and resid 23 through 41 Processing helix chain 'Q' and resid 42 through 53 removed outlier: 3.770A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 71 Processing helix chain 'Q' and resid 107 through 117 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'S' and resid 33 through 49 Processing helix chain 'S' and resid 52 through 56 Processing helix chain 'S' and resid 98 through 114 Processing helix chain 'S' and resid 117 through 119 No H-bonds generated for 'chain 'S' and resid 117 through 119' Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'W' and resid 20 through 34 removed outlier: 3.777A pdb=" N LEU W 34 " --> pdb=" O VAL W 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 59 Processing helix chain 'W' and resid 69 through 76 Processing helix chain 'W' and resid 108 through 119 Processing helix chain 'W' and resid 161 through 169 Processing helix chain 'W' and resid 198 through 207 removed outlier: 3.750A pdb=" N LEU W 203 " --> pdb=" O GLN W 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 22 Processing helix chain 'Y' and resid 23 through 31 removed outlier: 3.820A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 122 Processing helix chain 'b' and resid 62 through 67 removed outlier: 3.582A pdb=" N GLY b 67 " --> pdb=" O ASP b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 82 Processing helix chain 'b' and resid 87 through 97 Processing helix chain 'b' and resid 129 through 139 Processing helix chain 'b' and resid 147 through 160 removed outlier: 3.554A pdb=" N GLU b 151 " --> pdb=" O LEU b 147 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG b 159 " --> pdb=" O GLN b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 181 No H-bonds generated for 'chain 'b' and resid 179 through 181' Processing helix chain 'b' and resid 182 through 188 removed outlier: 3.898A pdb=" N THR b 188 " --> pdb=" O LEU b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 197 through 202 removed outlier: 3.506A pdb=" N THR b 201 " --> pdb=" O ALA b 198 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS b 202 " --> pdb=" O PHE b 199 " (cutoff:3.500A) Processing helix chain 'b' and resid 233 through 245 Processing helix chain 'b' and resid 265 through 275 removed outlier: 4.823A pdb=" N PHE b 271 " --> pdb=" O GLN b 267 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N HIS b 272 " --> pdb=" O VAL b 268 " (cutoff:3.500A) Processing helix chain 'b' and resid 276 through 282 removed outlier: 5.442A pdb=" N ASN b 280 " --> pdb=" O LEU b 277 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 342 removed outlier: 3.754A pdb=" N LEU b 340 " --> pdb=" O CYS b 336 " (cutoff:3.500A) Processing helix chain 'b' and resid 441 through 445 Processing helix chain 'b' and resid 449 through 466 Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 60 through 64 Processing helix chain 'e' and resid 78 through 84 removed outlier: 3.730A pdb=" N THR e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 89 removed outlier: 4.114A pdb=" N THR e 89 " --> pdb=" O THR e 86 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 4.167A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 43 removed outlier: 4.043A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 10 Processing helix chain 'h' and resid 13 through 33 removed outlier: 3.670A pdb=" N VAL h 33 " --> pdb=" O ALA h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 70 Processing helix chain 'h' and resid 85 through 90 removed outlier: 3.718A pdb=" N ARG h 89 " --> pdb=" O THR h 85 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG h 90 " --> pdb=" O ARG h 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 85 through 90' Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 35 through 49 Processing helix chain 'i' and resid 53 through 57 Processing helix chain 'j' and resid 50 through 58 Processing helix chain 'j' and resid 66 through 76 removed outlier: 3.739A pdb=" N VAL j 70 " --> pdb=" O TYR j 66 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'm' and resid 262 through 267 Processing helix chain 'm' and resid 269 through 285 removed outlier: 3.563A pdb=" N ALA m 273 " --> pdb=" O SER m 269 " (cutoff:3.500A) Processing helix chain 'm' and resid 290 through 298 Processing helix chain 'm' and resid 347 through 355 removed outlier: 3.860A pdb=" N GLU m 352 " --> pdb=" O PRO m 348 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA m 353 " --> pdb=" O GLU m 349 " (cutoff:3.500A) Processing helix chain 'n' and resid 17 through 25 Processing helix chain 'n' and resid 64 through 70 removed outlier: 4.432A pdb=" N TYR n 70 " --> pdb=" O LYS n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 73 No H-bonds generated for 'chain 'n' and resid 71 through 73' Processing helix chain 'n' and resid 83 through 97 removed outlier: 4.006A pdb=" N ALA n 87 " --> pdb=" O HIS n 83 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG n 88 " --> pdb=" O LYS n 84 " (cutoff:3.500A) Processing helix chain 'n' and resid 99 through 107 Processing helix chain 'n' and resid 115 through 122 removed outlier: 3.549A pdb=" N GLU n 120 " --> pdb=" O HIS n 116 " (cutoff:3.500A) Processing helix chain 'n' and resid 124 through 127 Processing helix chain 'n' and resid 128 through 145 removed outlier: 4.256A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 174 Processing helix chain 'n' and resid 214 through 239 removed outlier: 3.928A pdb=" N MET n 218 " --> pdb=" O ASP n 214 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE n 231 " --> pdb=" O THR n 227 " (cutoff:3.500A) Processing helix chain 'n' and resid 250 through 255 Processing helix chain 'n' and resid 354 through 359 Processing helix chain 'n' and resid 391 through 394 Processing helix chain 'n' and resid 428 through 437 removed outlier: 4.094A pdb=" N ILE n 432 " --> pdb=" O GLN n 428 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 115 removed outlier: 3.807A pdb=" N PHE o 111 " --> pdb=" O LEU o 107 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN o 113 " --> pdb=" O LYS o 109 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE o 114 " --> pdb=" O TYR o 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 141 through 152 Processing helix chain 'o' and resid 195 through 212 removed outlier: 4.103A pdb=" N ALA o 212 " --> pdb=" O ILE o 208 " (cutoff:3.500A) Processing helix chain 't' and resid 57 through 87 removed outlier: 4.265A pdb=" N ILE t 61 " --> pdb=" O ARG t 57 " (cutoff:3.500A) Processing helix chain 't' and resid 156 through 166 Processing helix chain 't' and resid 183 through 190 removed outlier: 3.882A pdb=" N VAL t 189 " --> pdb=" O PRO t 185 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE t 190 " --> pdb=" O LEU t 186 " (cutoff:3.500A) Processing helix chain 't' and resid 191 through 194 Processing helix chain 't' and resid 200 through 212 Processing helix chain 't' and resid 231 through 240 removed outlier: 3.971A pdb=" N VAL t 235 " --> pdb=" O ASP t 231 " (cutoff:3.500A) Processing helix chain 't' and resid 241 through 243 No H-bonds generated for 'chain 't' and resid 241 through 243' Processing helix chain 't' and resid 246 through 256 removed outlier: 3.590A pdb=" N ILE t 250 " --> pdb=" O CYS t 246 " (cutoff:3.500A) Processing helix chain 't' and resid 259 through 264 Processing helix chain 't' and resid 265 through 267 No H-bonds generated for 'chain 't' and resid 265 through 267' Processing helix chain 't' and resid 282 through 296 removed outlier: 4.186A pdb=" N LEU t 286 " --> pdb=" O SER t 282 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG t 287 " --> pdb=" O LEU t 283 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS t 288 " --> pdb=" O ASN t 284 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU t 293 " --> pdb=" O ILE t 289 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA t 294 " --> pdb=" O LYS t 290 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 45 through 49 removed outlier: 3.504A pdb=" N LEU u 49 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 57 Processing helix chain 'u' and resid 82 through 112 removed outlier: 3.511A pdb=" N THR u 89 " --> pdb=" O LEU u 85 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS u 91 " --> pdb=" O ALA u 87 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) Processing helix chain 'v' and resid 4 through 12 Processing helix chain 'v' and resid 21 through 27 removed outlier: 3.500A pdb=" N GLN v 25 " --> pdb=" O ASN v 21 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG v 26 " --> pdb=" O LYS v 22 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS v 27 " --> pdb=" O ASP v 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 21 through 27' Processing helix chain 'v' and resid 33 through 40 removed outlier: 3.547A pdb=" N ALA v 37 " --> pdb=" O ASN v 33 " (cutoff:3.500A) Processing helix chain 'v' and resid 45 through 54 Processing helix chain 'v' and resid 157 through 165 removed outlier: 3.702A pdb=" N LYS v 161 " --> pdb=" O GLU v 157 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU v 165 " --> pdb=" O LYS v 161 " (cutoff:3.500A) Processing helix chain 'v' and resid 178 through 193 Processing helix chain 'v' and resid 195 through 201 removed outlier: 3.643A pdb=" N PHE v 201 " --> pdb=" O LYS v 197 " (cutoff:3.500A) Processing helix chain 'v' and resid 211 through 226 Processing helix chain 'x' and resid 12 through 44 removed outlier: 3.805A pdb=" N GLU x 43 " --> pdb=" O LYS x 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 44 through 55 removed outlier: 3.712A pdb=" N ARG x 48 " --> pdb=" O ASN x 44 " (cutoff:3.500A) Processing helix chain 'x' and resid 60 through 64 Processing helix chain 'x' and resid 79 through 86 Processing helix chain 'x' and resid 104 through 118 Processing helix chain 'x' and resid 131 through 142 Processing helix chain 'x' and resid 204 through 218 Processing helix chain 'y' and resid 13 through 15 No H-bonds generated for 'chain 'y' and resid 13 through 15' Processing helix chain 'y' and resid 31 through 43 removed outlier: 3.589A pdb=" N TYR y 35 " --> pdb=" O SER y 31 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE y 38 " --> pdb=" O PHE y 34 " (cutoff:3.500A) Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 107 Processing helix chain 'y' and resid 124 through 134 Processing helix chain 'y' and resid 192 through 197 removed outlier: 3.698A pdb=" N MET y 197 " --> pdb=" O VAL y 193 " (cutoff:3.500A) Processing helix chain 'y' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain '3' and resid 18 through 20 Processing sheet with id=AA2, first strand: chain '3' and resid 50 through 55 removed outlier: 3.528A pdb=" N ILE 3 80 " --> pdb=" O LEU 3 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 135 through 136 Processing sheet with id=AA4, first strand: chain '5' and resid 34 through 38 removed outlier: 3.771A pdb=" N ALA 5 36 " --> pdb=" O GLU 5 15 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG 5 2 " --> pdb=" O LEU 5 410 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE 5 406 " --> pdb=" O SER 5 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 47 through 51 removed outlier: 6.540A pdb=" N VAL 5 67 " --> pdb=" O SER 5 113 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER 5 113 " --> pdb=" O VAL 5 67 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU 5 69 " --> pdb=" O THR 5 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 140 through 145 removed outlier: 3.840A pdb=" N THR 5 142 " --> pdb=" O ALA 5 158 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS 5 144 " --> pdb=" O VAL 5 156 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU 5 163 " --> pdb=" O THR 5 159 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA 5 179 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LYS 5 168 " --> pdb=" O LYS 5 177 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LYS 5 177 " --> pdb=" O LYS 5 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '5' and resid 189 through 192 removed outlier: 3.589A pdb=" N PHE 5 189 " --> pdb=" O GLY 5 208 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY 5 208 " --> pdb=" O PHE 5 189 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLY 5 209 " --> pdb=" O LEU 5 213 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU 5 213 " --> pdb=" O GLY 5 209 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP 5 230 " --> pdb=" O LEU 5 216 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLU 5 218 " --> pdb=" O GLN 5 228 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLN 5 228 " --> pdb=" O GLU 5 218 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '5' and resid 248 through 254 removed outlier: 4.416A pdb=" N GLN 5 269 " --> pdb=" O LEU 5 254 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N HIS 5 278 " --> pdb=" O THR 5 274 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA 5 292 " --> pdb=" O LYS 5 281 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '5' and resid 303 through 308 removed outlier: 5.198A pdb=" N GLN 5 305 " --> pdb=" O THR 5 336 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR 5 336 " --> pdb=" O GLN 5 305 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL 5 342 " --> pdb=" O LYS 5 354 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS 5 354 " --> pdb=" O VAL 5 342 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS 5 344 " --> pdb=" O LEU 5 352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '5' and resid 366 through 370 removed outlier: 6.699A pdb=" N ASP 5 388 " --> pdb=" O MET 5 394 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N MET 5 394 " --> pdb=" O ASP 5 388 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 358 through 359 removed outlier: 7.017A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA B 217 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE B 278 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N THR B 276 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE B 282 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS B 325 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG B 70 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP B 59 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 72 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL B 57 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLU B 74 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N THR B 55 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 76 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N MET B 53 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 98 through 106 removed outlier: 7.193A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B 157 " --> pdb=" O TYR B 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 98 through 106 removed outlier: 7.193A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 9 removed outlier: 6.748A pdb=" N VAL C 6 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASN C 18 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL C 8 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 62 through 63 Processing sheet with id=AB7, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.043A pdb=" N LEU C 150 " --> pdb=" O TRP C 250 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB9, first strand: chain 'D' and resid 82 through 84 removed outlier: 6.486A pdb=" N VAL D 82 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 194 " --> pdb=" O ILE D 118 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE D 117 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ALA D 170 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL D 119 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 392 through 394 removed outlier: 6.597A pdb=" N GLN D 266 " --> pdb=" O ASN D 413 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 317 through 319 removed outlier: 4.002A pdb=" N THR D 346 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE D 292 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N CYS D 345 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL D 294 " --> pdb=" O CYS D 345 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 77 through 79 removed outlier: 3.533A pdb=" N ARG E 77 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 65 " --> pdb=" O ARG E 77 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU E 64 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.269A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY F 230 " --> pdb=" O VAL F 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AC6, first strand: chain 'G' and resid 177 through 180 removed outlier: 6.297A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU G 150 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.654A pdb=" N LYS H 26 " --> pdb=" O SER H 19 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 144 through 148 removed outlier: 6.468A pdb=" N LYS H 89 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 243 through 250 removed outlier: 6.857A pdb=" N GLN K 79 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 97 through 101 Processing sheet with id=AD3, first strand: chain 'K' and resid 153 through 156 Processing sheet with id=AD4, first strand: chain 'K' and resid 212 through 213 Processing sheet with id=AD5, first strand: chain 'L' and resid 23 through 24 removed outlier: 6.306A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AD7, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AD8, first strand: chain 'M' and resid 53 through 59 removed outlier: 5.325A pdb=" N GLY M 48 " --> pdb=" O PRO M 54 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN M 56 " --> pdb=" O ILE M 46 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE M 46 " --> pdb=" O GLN M 56 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.302A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE N 130 " --> pdb=" O VAL N 64 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR N 127 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLN N 123 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL N 135 " --> pdb=" O VAL N 115 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL N 115 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 6 through 10 Processing sheet with id=AE2, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AE3, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.692A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR P 151 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL P 114 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AE5, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AE6, first strand: chain 'Q' and resid 120 through 122 Processing sheet with id=AE7, first strand: chain 'S' and resid 25 through 31 removed outlier: 7.202A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 87 through 96 removed outlier: 3.930A pdb=" N TYR S 81 " --> pdb=" O HIS S 88 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS S 125 " --> pdb=" O TRP S 78 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP S 82 " --> pdb=" O ILE S 121 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE S 121 " --> pdb=" O ASP S 82 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 65 through 66 removed outlier: 3.711A pdb=" N THR W 105 " --> pdb=" O TYR W 39 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR W 39 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR W 221 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 32 through 34 removed outlier: 3.604A pdb=" N ALA Y 33 " --> pdb=" O LEU Y 48 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU Y 48 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'Y' and resid 79 through 82 removed outlier: 4.005A pdb=" N SER Y 72 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU Y 55 " --> pdb=" O THR Y 107 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 86 through 88 Processing sheet with id=AF4, first strand: chain 'b' and resid 205 through 211 Processing sheet with id=AF5, first strand: chain 'b' and resid 251 through 254 removed outlier: 3.547A pdb=" N VAL b 286 " --> pdb=" O TYR b 252 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET b 254 " --> pdb=" O VAL b 286 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'b' and resid 435 through 436 Processing sheet with id=AF7, first strand: chain 'e' and resid 72 through 76 removed outlier: 6.014A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'f' and resid 8 through 18 removed outlier: 7.035A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR f 16 " --> pdb=" O VAL f 27 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL f 27 " --> pdb=" O TYR f 16 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N ARG f 18 " --> pdb=" O PRO f 25 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AG1, first strand: chain 'n' and resid 178 through 181 removed outlier: 3.827A pdb=" N LYS n 178 " --> pdb=" O GLN n 189 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL n 201 " --> pdb=" O VAL n 186 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'n' and resid 388 through 389 removed outlier: 6.553A pdb=" N TYR n 366 " --> pdb=" O ILE n 411 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'o' and resid 117 through 124 removed outlier: 5.119A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN o 163 " --> pdb=" O SER o 96 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR o 155 " --> pdb=" O LEU o 162 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 't' and resid 133 through 134 Processing sheet with id=AG5, first strand: chain 'u' and resid 4 through 5 removed outlier: 3.686A pdb=" N TYR u 4 " --> pdb=" O CYS u 13 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'x' and resid 121 through 123 removed outlier: 3.572A pdb=" N THR x 122 " --> pdb=" O ILE x 95 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE x 150 " --> pdb=" O THR x 98 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY x 159 " --> pdb=" O ASN x 151 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR x 158 " --> pdb=" O LEU x 175 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER x 176 " --> pdb=" O THR x 264 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR x 264 " --> pdb=" O SER x 176 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE x 178 " --> pdb=" O GLN x 262 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN x 262 " --> pdb=" O PHE x 178 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLU x 196 " --> pdb=" O ILE x 230 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU x 232 " --> pdb=" O GLU x 196 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE x 198 " --> pdb=" O LEU x 232 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASN x 234 " --> pdb=" O ILE x 198 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN x 200 " --> pdb=" O ASN x 234 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'x' and resid 121 through 123 removed outlier: 3.572A pdb=" N THR x 122 " --> pdb=" O ILE x 95 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE x 150 " --> pdb=" O THR x 98 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY x 159 " --> pdb=" O ASN x 151 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR x 158 " --> pdb=" O LEU x 175 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER x 176 " --> pdb=" O THR x 264 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR x 264 " --> pdb=" O SER x 176 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE x 178 " --> pdb=" O GLN x 262 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN x 262 " --> pdb=" O PHE x 178 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'y' and resid 2 through 5 removed outlier: 6.285A pdb=" N THR y 3 " --> pdb=" O THR y 206 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'y' and resid 17 through 19 removed outlier: 6.664A pdb=" N CYS y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'y' and resid 64 through 65 removed outlier: 3.744A pdb=" N ALA y 64 " --> pdb=" O LEU y 71 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'y' and resid 109 through 110 removed outlier: 3.547A pdb=" N CYS y 109 " --> pdb=" O LEU y 116 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'y' and resid 152 through 155 removed outlier: 3.506A pdb=" N GLY y 158 " --> pdb=" O SER y 155 " (cutoff:3.500A) 2064 hydrogen bonds defined for protein. 5832 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1319 hydrogen bonds 2132 hydrogen bond angles 0 basepair planarities 531 basepair parallelities 786 stacking parallelities Total time for adding SS restraints: 89.41 Time building geometry restraints manager: 112.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.25: 79578 1.25 - 1.67: 82590 1.67 - 2.08: 202 2.08 - 2.50: 0 2.50 - 2.91: 1 Bond restraints: 162371 Sorted by residual: bond pdb=" O3' G 1 779 " pdb=" P G 1 781 " ideal model delta sigma weight residual 1.607 2.913 -1.306 1.50e-02 4.44e+03 7.58e+03 bond pdb=" N GLY N 2 " pdb=" CA GLY N 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.29e+00 bond pdb=" N ARG W 3 " pdb=" CA ARG W 3 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N HIS Q 15 " pdb=" CA HIS Q 15 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N ALA h 2 " pdb=" CA ALA h 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 ... (remaining 162366 not shown) Histogram of bond angle deviations from ideal: 58.69 - 73.79: 2 73.79 - 88.88: 0 88.88 - 103.97: 5729 103.97 - 119.06: 216140 119.06 - 134.15: 70882 Bond angle restraints: 292753 Sorted by residual: angle pdb=" O3' G 1 779 " pdb=" P G 1 781 " pdb=" O5' G 1 781 " ideal model delta sigma weight residual 104.00 58.98 45.02 1.50e+00 4.44e-01 9.01e+02 angle pdb=" O3' G 1 779 " pdb=" P G 1 781 " pdb=" OP2 G 1 781 " ideal model delta sigma weight residual 108.00 58.69 49.31 3.00e+00 1.11e-01 2.70e+02 angle pdb=" C3' G 1 779 " pdb=" O3' G 1 779 " pdb=" P G 1 781 " ideal model delta sigma weight residual 120.20 106.35 13.85 1.50e+00 4.44e-01 8.53e+01 angle pdb=" N VAL b 411 " pdb=" CA VAL b 411 " pdb=" C VAL b 411 " ideal model delta sigma weight residual 113.71 109.73 3.98 9.50e-01 1.11e+00 1.75e+01 angle pdb=" O3' G 11097 " pdb=" C3' G 11097 " pdb=" C2' G 11097 " ideal model delta sigma weight residual 109.50 115.54 -6.04 1.50e+00 4.44e-01 1.62e+01 ... (remaining 292748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 62393 35.93 - 71.86: 1859 71.86 - 107.80: 203 107.80 - 143.73: 27 143.73 - 179.66: 49 Dihedral angle restraints: 64531 sinusoidal: 43868 harmonic: 20663 Sorted by residual: dihedral pdb=" C4' A 11200 " pdb=" C3' A 11200 " pdb=" C2' A 11200 " pdb=" C1' A 11200 " ideal model delta sinusoidal sigma weight residual -35.00 36.54 -71.54 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' G 11097 " pdb=" C3' G 11097 " pdb=" C2' G 11097 " pdb=" C1' G 11097 " ideal model delta sinusoidal sigma weight residual -35.00 36.07 -71.07 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' A 1 352 " pdb=" C3' A 1 352 " pdb=" C2' A 1 352 " pdb=" C1' A 1 352 " ideal model delta sinusoidal sigma weight residual -35.00 35.64 -70.64 1 8.00e+00 1.56e-02 1.00e+02 ... (remaining 64528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 15297 0.063 - 0.126: 956 0.126 - 0.189: 34 0.189 - 0.253: 51 0.253 - 0.316: 8 Chirality restraints: 16346 Sorted by residual: chirality pdb=" C3' G 11097 " pdb=" C4' G 11097 " pdb=" O3' G 11097 " pdb=" C2' G 11097 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" C3' G 11242 " pdb=" C4' G 11242 " pdb=" O3' G 11242 " pdb=" C2' G 11242 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C3' G 1 770 " pdb=" C4' G 1 770 " pdb=" O3' G 1 770 " pdb=" C2' G 1 770 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 16343 not shown) Planarity restraints: 17284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 2 14 " -0.036 2.00e-02 2.50e+03 1.68e-02 7.77e+00 pdb=" N1 C 2 14 " 0.039 2.00e-02 2.50e+03 pdb=" C2 C 2 14 " 0.000 2.00e-02 2.50e+03 pdb=" O2 C 2 14 " 0.006 2.00e-02 2.50e+03 pdb=" N3 C 2 14 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C 2 14 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C 2 14 " -0.011 2.00e-02 2.50e+03 pdb=" C5 C 2 14 " 0.010 2.00e-02 2.50e+03 pdb=" C6 C 2 14 " 0.002 2.00e-02 2.50e+03 pdb=" H5 C 2 14 " -0.006 2.00e-02 2.50e+03 pdb=" H6 C 2 14 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 15 " 0.034 2.00e-02 2.50e+03 1.32e-02 6.09e+00 pdb=" N9 G 2 15 " -0.032 2.00e-02 2.50e+03 pdb=" C8 G 2 15 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G 2 15 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 2 15 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G 2 15 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G 2 15 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G 2 15 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G 2 15 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G 2 15 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G 2 15 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G 2 15 " -0.002 2.00e-02 2.50e+03 pdb=" H8 G 2 15 " -0.002 2.00e-02 2.50e+03 pdb=" H1 G 2 15 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 13212 " 0.031 2.00e-02 2.50e+03 1.46e-02 5.86e+00 pdb=" N1 C 13212 " -0.030 2.00e-02 2.50e+03 pdb=" C2 C 13212 " 0.006 2.00e-02 2.50e+03 pdb=" O2 C 13212 " -0.011 2.00e-02 2.50e+03 pdb=" N3 C 13212 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C 13212 " 0.012 2.00e-02 2.50e+03 pdb=" N4 C 13212 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C 13212 " -0.008 2.00e-02 2.50e+03 pdb=" C6 C 13212 " -0.003 2.00e-02 2.50e+03 pdb=" H5 C 13212 " 0.004 2.00e-02 2.50e+03 pdb=" H6 C 13212 " -0.006 2.00e-02 2.50e+03 ... (remaining 17281 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 6405 2.16 - 2.77: 266257 2.77 - 3.38: 425498 3.38 - 3.99: 565508 3.99 - 4.60: 857278 Nonbonded interactions: 2120946 Sorted by model distance: nonbonded pdb=" H21 G 11404 " pdb=" OP2 A 11407 " model vdw 1.551 1.850 nonbonded pdb=" OP2 G 1 297 " pdb=" H22 G 1 297 " model vdw 1.572 1.850 nonbonded pdb=" OP1 U 1 594 " pdb=" H1 G 1 609 " model vdw 1.578 1.850 nonbonded pdb=" OD1 ASN y 111 " pdb=" H VAL y 114 " model vdw 1.578 1.850 nonbonded pdb=" OP2 U 13214 " pdb="HH22 ARG M 128 " model vdw 1.580 1.850 ... (remaining 2120941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1774 5.49 5 S 123 5.16 5 C 48264 2.51 5 N 15763 2.21 5 O 21063 1.98 5 H 70039 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.540 Extract box with map and model: 24.030 Check model and map are aligned: 1.830 Convert atoms to be neutral: 1.030 Process input model: 493.980 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.400 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: 0.030 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 532.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 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 : 0.005 1.306 92332 Z= 0.238 Angle : 0.493 49.306 133069 Z= 0.256 Chirality : 0.034 0.316 16346 Planarity : 0.002 0.051 10207 Dihedral : 16.089 179.660 40312 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.12), residues: 5868 helix: 2.36 (0.12), residues: 2287 sheet: 0.28 (0.18), residues: 828 loop : -0.06 (0.12), residues: 2753 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1411 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1368 time to evaluate : 7.917 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 43 outliers final: 17 residues processed: 1403 average time/residue: 2.1037 time to fit residues: 4837.3414 Evaluate side-chains 882 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 865 time to evaluate : 7.762 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 2 residues processed: 17 average time/residue: 1.5737 time to fit residues: 57.5929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 649 optimal weight: 20.0000 chunk 582 optimal weight: 50.0000 chunk 323 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 393 optimal weight: 5.9990 chunk 311 optimal weight: 0.8980 chunk 602 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 chunk 366 optimal weight: 10.0000 chunk 448 optimal weight: 7.9990 chunk 698 optimal weight: 40.0000 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 73 HIS ** 5 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 269 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN C 116 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN C 260 GLN D 178 HIS D 330 ASN D 441 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS F 194 HIS H 59 ASN K 262 ASN P 121 GLN Q 45 ASN Q 58 ASN S 62 ASN S 142 GLN W 22 ASN e 98 HIS ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 59 ASN h 99 GLN j 76 ASN o 113 GLN t 154 ASN ** u 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 25 GLN v 39 ASN x 102 ASN x 187 HIS ** y 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.225 92332 Z= 0.280 Angle : 0.583 17.578 133069 Z= 0.308 Chirality : 0.036 0.221 16346 Planarity : 0.004 0.096 10207 Dihedral : 15.108 179.453 27800 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.30 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.11), residues: 5868 helix: 1.77 (0.11), residues: 2323 sheet: -0.20 (0.17), residues: 846 loop : -0.34 (0.12), residues: 2699 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 873 time to evaluate : 7.810 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 outliers start: 95 outliers final: 60 residues processed: 937 average time/residue: 1.9621 time to fit residues: 3041.0986 Evaluate side-chains 837 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 777 time to evaluate : 7.029 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 1.4659 time to fit residues: 165.8196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 388 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 581 optimal weight: 7.9990 chunk 475 optimal weight: 9.9990 chunk 192 optimal weight: 0.9980 chunk 699 optimal weight: 20.0000 chunk 755 optimal weight: 30.0000 chunk 623 optimal weight: 3.9990 chunk 693 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 561 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 26 ASN ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN H 58 HIS H 59 ASN ** K 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 284 ASN M 41 GLN O 42 ASN ** S 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS o 113 GLN ** y 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.331 92332 Z= 0.281 Angle : 0.542 16.079 133069 Z= 0.288 Chirality : 0.036 0.280 16346 Planarity : 0.004 0.091 10207 Dihedral : 15.227 179.743 27800 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.02 % 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: 0.44 (0.11), residues: 5868 helix: 1.58 (0.11), residues: 2314 sheet: -0.44 (0.17), residues: 833 loop : -0.56 (0.12), residues: 2721 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 807 time to evaluate : 6.971 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 outliers start: 63 outliers final: 36 residues processed: 841 average time/residue: 1.9973 time to fit residues: 2796.3380 Evaluate side-chains 783 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 747 time to evaluate : 7.806 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 36 outliers final: 1 residues processed: 36 average time/residue: 1.5972 time to fit residues: 112.8559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 691 optimal weight: 20.0000 chunk 525 optimal weight: 0.9980 chunk 363 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 333 optimal weight: 20.0000 chunk 469 optimal weight: 7.9990 chunk 702 optimal weight: 40.0000 chunk 743 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 chunk 665 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 26 ASN ** 5 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 GLN H 59 ASN ** K 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 HIS ** S 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 ASN ** S 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 22 ASN ** f 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN ** y 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.214 92332 Z= 0.350 Angle : 0.611 13.870 133069 Z= 0.324 Chirality : 0.038 0.283 16346 Planarity : 0.005 0.081 10207 Dihedral : 15.522 179.810 27800 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.00 % Favored : 93.92 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.11), residues: 5868 helix: 1.14 (0.11), residues: 2321 sheet: -0.83 (0.17), residues: 836 loop : -0.87 (0.12), residues: 2711 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 767 time to evaluate : 7.399 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 outliers start: 85 outliers final: 53 residues processed: 821 average time/residue: 1.9237 time to fit residues: 2621.6629 Evaluate side-chains 766 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 713 time to evaluate : 7.864 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 3 residues processed: 53 average time/residue: 1.6252 time to fit residues: 162.1168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 619 optimal weight: 10.0000 chunk 421 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 553 optimal weight: 30.0000 chunk 306 optimal weight: 1.9990 chunk 634 optimal weight: 9.9990 chunk 513 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 379 optimal weight: 0.9990 chunk 667 optimal weight: 4.9990 chunk 187 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 26 ASN ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 234 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN H 183 HIS ** K 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN ** S 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 22 ASN e 35 GLN y 9 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.143 92332 Z= 0.266 Angle : 0.544 12.753 133069 Z= 0.289 Chirality : 0.036 0.249 16346 Planarity : 0.004 0.077 10207 Dihedral : 15.618 179.931 27800 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.42 % Favored : 94.51 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.11), residues: 5868 helix: 1.25 (0.11), residues: 2323 sheet: -0.83 (0.17), residues: 827 loop : -0.88 (0.12), residues: 2718 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 734 time to evaluate : 7.313 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 outliers start: 64 outliers final: 36 residues processed: 772 average time/residue: 1.8326 time to fit residues: 2341.1120 Evaluate side-chains 740 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 704 time to evaluate : 7.162 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 3 residues processed: 36 average time/residue: 1.4826 time to fit residues: 103.9873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 250 optimal weight: 20.0000 chunk 669 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 436 optimal weight: 30.0000 chunk 183 optimal weight: 10.0000 chunk 744 optimal weight: 9.9990 chunk 617 optimal weight: 9.9990 chunk 344 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 246 optimal weight: 40.0000 chunk 390 optimal weight: 4.9990 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 GLN ** S 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 22 ASN ** n 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.112 92332 Z= 0.442 Angle : 0.674 7.265 133069 Z= 0.356 Chirality : 0.041 0.244 16346 Planarity : 0.005 0.080 10207 Dihedral : 16.034 179.571 27800 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.40 % Favored : 92.52 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.11), residues: 5868 helix: 0.55 (0.10), residues: 2336 sheet: -1.08 (0.17), residues: 812 loop : -1.29 (0.12), residues: 2720 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 694 time to evaluate : 7.882 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 outliers start: 74 outliers final: 54 residues processed: 739 average time/residue: 1.7880 time to fit residues: 2185.9377 Evaluate side-chains 720 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 666 time to evaluate : 6.999 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 3 residues processed: 54 average time/residue: 1.3461 time to fit residues: 140.5897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 717 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 423 optimal weight: 20.0000 chunk 543 optimal weight: 4.9990 chunk 420 optimal weight: 30.0000 chunk 626 optimal weight: 10.0000 chunk 415 optimal weight: 10.0000 chunk 741 optimal weight: 20.0000 chunk 463 optimal weight: 7.9990 chunk 451 optimal weight: 0.8980 chunk 342 optimal weight: 20.0000 overall best weight: 6.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 25 GLN ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 34 HIS B 280 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN ** n 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 226 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 92332 Z= 0.313 Angle : 0.586 6.684 133069 Z= 0.311 Chirality : 0.038 0.254 16346 Planarity : 0.004 0.082 10207 Dihedral : 16.109 179.718 27800 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.32 % Favored : 93.61 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.11), residues: 5868 helix: 0.77 (0.11), residues: 2336 sheet: -1.19 (0.17), residues: 829 loop : -1.21 (0.12), residues: 2703 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 696 time to evaluate : 7.132 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 outliers start: 40 outliers final: 24 residues processed: 719 average time/residue: 1.7629 time to fit residues: 2093.0515 Evaluate side-chains 705 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 681 time to evaluate : 7.003 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 4 residues processed: 24 average time/residue: 1.5543 time to fit residues: 71.2837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 458 optimal weight: 0.9990 chunk 295 optimal weight: 5.9990 chunk 442 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 471 optimal weight: 6.9990 chunk 504 optimal weight: 10.0000 chunk 366 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 582 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 22 ASN ** n 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 92332 Z= 0.336 Angle : 0.603 8.321 133069 Z= 0.320 Chirality : 0.038 0.273 16346 Planarity : 0.004 0.081 10207 Dihedral : 16.208 179.715 27800 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.65 % Favored : 92.28 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.11), residues: 5868 helix: 0.69 (0.11), residues: 2342 sheet: -1.21 (0.17), residues: 822 loop : -1.27 (0.12), residues: 2704 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 692 time to evaluate : 7.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 32 residues processed: 722 average time/residue: 1.6982 time to fit residues: 2024.4103 Evaluate side-chains 708 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 676 time to evaluate : 7.055 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 4 residues processed: 32 average time/residue: 1.4183 time to fit residues: 88.1772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 674 optimal weight: 8.9990 chunk 710 optimal weight: 30.0000 chunk 647 optimal weight: 7.9990 chunk 690 optimal weight: 9.9990 chunk 709 optimal weight: 8.9990 chunk 415 optimal weight: 10.0000 chunk 300 optimal weight: 5.9990 chunk 542 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 624 optimal weight: 10.0000 chunk 653 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 22 ASN ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 282 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 92332 Z= 0.316 Angle : 0.594 7.483 133069 Z= 0.315 Chirality : 0.038 0.274 16346 Planarity : 0.004 0.080 10207 Dihedral : 16.276 179.117 27800 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.31 % Favored : 92.62 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.11), residues: 5868 helix: 0.70 (0.11), residues: 2341 sheet: -1.20 (0.17), residues: 811 loop : -1.29 (0.12), residues: 2716 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 695 time to evaluate : 7.028 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 outliers start: 33 outliers final: 23 residues processed: 710 average time/residue: 1.6962 time to fit residues: 1984.0264 Evaluate side-chains 692 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 669 time to evaluate : 7.543 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 5 residues processed: 23 average time/residue: 1.5117 time to fit residues: 68.1840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 688 optimal weight: 20.0000 chunk 453 optimal weight: 5.9990 chunk 730 optimal weight: 9.9990 chunk 445 optimal weight: 20.0000 chunk 346 optimal weight: 8.9990 chunk 507 optimal weight: 10.0000 chunk 766 optimal weight: 40.0000 chunk 705 optimal weight: 20.0000 chunk 610 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 471 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 22 ASN ** n 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.907 92332 Z= 0.469 Angle : 0.676 106.071 133069 Z= 0.336 Chirality : 0.038 0.400 16346 Planarity : 0.004 0.081 10207 Dihedral : 16.277 179.110 27800 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.50 % Favored : 92.43 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.11), residues: 5868 helix: 0.68 (0.11), residues: 2340 sheet: -1.20 (0.17), residues: 811 loop : -1.30 (0.12), residues: 2717 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 669 time to evaluate : 7.478 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 outliers start: 28 outliers final: 27 residues processed: 680 average time/residue: 1.6966 time to fit residues: 1902.4107 Evaluate side-chains 693 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 666 time to evaluate : 7.121 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 5 residues processed: 27 average time/residue: 1.4863 time to fit residues: 78.1647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 374 optimal weight: 0.8980 chunk 484 optimal weight: 9.9990 chunk 649 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 562 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 611 optimal weight: 3.9990 chunk 255 optimal weight: 9.9990 chunk 627 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.087478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.068074 restraints weight = 1377351.221| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.81 r_work: 0.3497 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work: 0.3477 rms_B_bonded: 3.68 restraints_weight: 0.1250 r_work: 0.3467 rms_B_bonded: 3.74 restraints_weight: 0.0625 r_work: 0.3457 rms_B_bonded: 3.83 restraints_weight: 0.0312 r_work: 0.3446 rms_B_bonded: 3.96 restraints_weight: 0.0156 r_work: 0.3436 rms_B_bonded: 4.10 restraints_weight: 0.0078 r_work: 0.3424 rms_B_bonded: 4.27 restraints_weight: 0.0039 r_work: 0.3413 rms_B_bonded: 4.47 restraints_weight: 0.0020 r_work: 0.3400 rms_B_bonded: 4.70 restraints_weight: 0.0010 r_work: 0.3387 rms_B_bonded: 4.96 restraints_weight: 0.0005 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4107 r_free = 0.4107 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4068 r_free = 0.4068 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.4068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.907 92332 Z= 0.469 Angle : 0.676 106.070 133069 Z= 0.336 Chirality : 0.038 0.400 16346 Planarity : 0.004 0.081 10207 Dihedral : 16.277 179.110 27800 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.50 % Favored : 92.43 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.11), residues: 5868 helix: 0.68 (0.11), residues: 2340 sheet: -1.20 (0.17), residues: 811 loop : -1.30 (0.12), residues: 2717 =============================================================================== Job complete usr+sys time: 47638.43 seconds wall clock time: 808 minutes 49.87 seconds (48529.87 seconds total)