Starting phenix.real_space_refine (version: dev) on Mon Dec 19 01:35:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o71_12742/12_2022/7o71_12742_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o71_12742/12_2022/7o71_12742.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o71_12742/12_2022/7o71_12742_updated_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o71_12742/12_2022/7o71_12742_updated_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o71_12742/12_2022/7o71_12742_updated_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o71_12742/12_2022/7o71_12742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o71_12742/12_2022/7o71_12742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o71_12742/12_2022/7o71_12742_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o71_12742/12_2022/7o71_12742_updated_updated.pdb" } resolution = 2.4 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= 0.003 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 "A GLU 36": "OE1" <-> "OE2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A ASP 408": "OD1" <-> "OD2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ASP 556": "OD1" <-> "OD2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A ASP 720": "OD1" <-> "OD2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B GLU 458": "OE1" <-> "OE2" Residue "B GLU 474": "OE1" <-> "OE2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C ASP 353": "OD1" <-> "OD2" Residue "C GLU 404": "OE1" <-> "OE2" Residue "C PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "G ARG 43": "NH1" <-> "NH2" Residue "G GLU 52": "OE1" <-> "OE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G ARG 113": "NH1" <-> "NH2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "G ARG 223": "NH1" <-> "NH2" Residue "G ARG 230": "NH1" <-> "NH2" Residue "G ARG 259": "NH1" <-> "NH2" Residue "G ARG 262": "NH1" <-> "NH2" Residue "H GLU 37": "OE1" <-> "OE2" Residue "H GLU 50": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 116": "NH1" <-> "NH2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "H GLU 186": "OE1" <-> "OE2" Residue "H ARG 215": "NH1" <-> "NH2" Residue "H GLU 219": "OE1" <-> "OE2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I ARG 115": "NH1" <-> "NH2" Residue "I GLU 117": "OE1" <-> "OE2" Residue "I GLU 127": "OE1" <-> "OE2" Residue "I ARG 129": "NH1" <-> "NH2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I GLU 195": "OE1" <-> "OE2" Residue "I GLU 199": "OE1" <-> "OE2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K ARG 102": "NH1" <-> "NH2" Residue "K GLU 140": "OE1" <-> "OE2" Residue "K GLU 185": "OE1" <-> "OE2" Residue "K ARG 196": "NH1" <-> "NH2" Residue "K ARG 199": "NH1" <-> "NH2" Residue "K ARG 209": "NH1" <-> "NH2" Residue "L PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 19": "NH1" <-> "NH2" Residue "L ARG 20": "NH1" <-> "NH2" Residue "L GLU 30": "OE1" <-> "OE2" Residue "L GLU 66": "OE1" <-> "OE2" Residue "L ARG 79": "NH1" <-> "NH2" Residue "S ARG 49": "NH1" <-> "NH2" Residue "S ARG 62": "NH1" <-> "NH2" Residue "S GLU 85": "OE1" <-> "OE2" Residue "S GLU 87": "OE1" <-> "OE2" Residue "S ARG 120": "NH1" <-> "NH2" Residue "S GLU 153": "OE1" <-> "OE2" Residue "S ARG 156": "NH1" <-> "NH2" Residue "S GLU 160": "OE1" <-> "OE2" Residue "S ARG 188": "NH1" <-> "NH2" Residue "S GLU 189": "OE1" <-> "OE2" Residue "S GLU 224": "OE1" <-> "OE2" Residue "j ARG 39": "NH1" <-> "NH2" Residue "j TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 44": "OE1" <-> "OE2" Residue "j ARG 50": "NH1" <-> "NH2" Residue "j GLU 79": "OE1" <-> "OE2" Residue "j GLU 87": "OE1" <-> "OE2" Residue "1 GLU 7": "OE1" <-> "OE2" Residue "1 GLU 61": "OE1" <-> "OE2" Residue "1 GLU 67": "OE1" <-> "OE2" Residue "1 PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 147": "OE1" <-> "OE2" Residue "1 ARG 174": "NH1" <-> "NH2" Residue "1 GLU 206": "OE1" <-> "OE2" Residue "1 GLU 208": "OE1" <-> "OE2" Residue "1 GLU 231": "OE1" <-> "OE2" Residue "1 GLU 274": "OE1" <-> "OE2" Residue "2 ARG 22": "NH1" <-> "NH2" Residue "2 TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 226": "OE1" <-> "OE2" Residue "2 GLU 306": "OE1" <-> "OE2" Residue "2 GLU 433": "OE1" <-> "OE2" Residue "3 GLU 69": "OE1" <-> "OE2" Residue "4 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 162": "NH1" <-> "NH2" Residue "4 GLU 237": "OE1" <-> "OE2" Residue "4 ASP 352": "OD1" <-> "OD2" Residue "4 ARG 353": "NH1" <-> "NH2" Residue "4 GLU 395": "OE1" <-> "OE2" Residue "4 PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 405": "NH1" <-> "NH2" Residue "4 ARG 449": "NH1" <-> "NH2" Residue "5 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 63": "OE1" <-> "OE2" Residue "5 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 175": "NH1" <-> "NH2" Residue "5 GLU 241": "OE1" <-> "OE2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 GLU 453": "OE1" <-> "OE2" Residue "5 ARG 586": "NH1" <-> "NH2" Residue "5 ARG 611": "NH1" <-> "NH2" Residue "5 PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 17": "NH1" <-> "NH2" Residue "g ARG 47": "NH1" <-> "NH2" Residue "g ARG 69": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 35": "NH1" <-> "NH2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E ARG 201": "NH1" <-> "NH2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E ARG 281": "NH1" <-> "NH2" Residue "E GLU 288": "OE1" <-> "OE2" Residue "E GLU 315": "OE1" <-> "OE2" Residue "E GLU 339": "OE1" <-> "OE2" Residue "F ARG 26": "NH1" <-> "NH2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F GLU 112": "OE1" <-> "OE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "J ARG 91": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 177": "OE1" <-> "OE2" Residue "J GLU 181": "OE1" <-> "OE2" Residue "J ARG 183": "NH1" <-> "NH2" Residue "M GLU 30": "OE1" <-> "OE2" Residue "M GLU 34": "OE1" <-> "OE2" Residue "M ARG 42": "NH1" <-> "NH2" Residue "M GLU 55": "OE1" <-> "OE2" Residue "M GLU 65": "OE1" <-> "OE2" Residue "M ASP 68": "OD1" <-> "OD2" Residue "M GLU 80": "OE1" <-> "OE2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M ASP 98": "OD1" <-> "OD2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "M GLU 135": "OE1" <-> "OE2" Residue "O ARG 35": "NH1" <-> "NH2" Residue "O GLU 77": "OE1" <-> "OE2" Residue "P ARG 30": "NH1" <-> "NH2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "P PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 57": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 82": "OE1" <-> "OE2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "R ARG 37": "NH1" <-> "NH2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 57": "NH1" <-> "NH2" Residue "R GLU 91": "OE1" <-> "OE2" Residue "R ARG 92": "NH1" <-> "NH2" Residue "R ARG 97": "NH1" <-> "NH2" Residue "R GLU 99": "OE1" <-> "OE2" Residue "U GLU 27": "OE1" <-> "OE2" Residue "U GLU 59": "OE1" <-> "OE2" Residue "U GLU 71": "OE1" <-> "OE2" Residue "U ARG 73": "NH1" <-> "NH2" Residue "U ARG 74": "NH1" <-> "NH2" Residue "U ASP 92": "OD1" <-> "OD2" Residue "U GLU 93": "OE1" <-> "OE2" Residue "U GLU 102": "OE1" <-> "OE2" Residue "U ARG 112": "NH1" <-> "NH2" Residue "U GLU 139": "OE1" <-> "OE2" Residue "U ARG 161": "NH1" <-> "NH2" Residue "W ARG 20": "NH1" <-> "NH2" Residue "W ARG 21": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 29": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W GLU 54": "OE1" <-> "OE2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 66": "NH1" <-> "NH2" Residue "W ARG 83": "NH1" <-> "NH2" Residue "W ARG 84": "NH1" <-> "NH2" Residue "W ARG 91": "NH1" <-> "NH2" Residue "X GLU 58": "OE1" <-> "OE2" Residue "X ARG 69": "NH1" <-> "NH2" Residue "X ARG 76": "NH1" <-> "NH2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X GLU 137": "OE1" <-> "OE2" Residue "X GLU 167": "OE1" <-> "OE2" Residue "Y GLU 72": "OE1" <-> "OE2" Residue "Y ARG 79": "NH1" <-> "NH2" Residue "Y GLU 92": "OE1" <-> "OE2" Residue "Y PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 140": "NH1" <-> "NH2" Residue "Y ARG 159": "NH1" <-> "NH2" Residue "Z GLU 22": "OE1" <-> "OE2" Residue "Z ARG 77": "NH1" <-> "NH2" Residue "Z ARG 80": "NH1" <-> "NH2" Residue "Z ARG 81": "NH1" <-> "NH2" Residue "Z GLU 112": "OE1" <-> "OE2" Residue "Z GLU 143": "OE1" <-> "OE2" Residue "Z GLU 166": "OE1" <-> "OE2" Residue "Z GLU 168": "OE1" <-> "OE2" Residue "Z ARG 179": "NH1" <-> "NH2" Residue "a GLU 33": "OE1" <-> "OE2" Residue "a GLU 34": "OE1" <-> "OE2" Residue "a ASP 62": "OD1" <-> "OD2" Residue "a GLU 68": "OE1" <-> "OE2" Residue "a ARG 123": "NH1" <-> "NH2" Residue "a GLU 124": "OE1" <-> "OE2" Residue "a PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 147": "NH1" <-> "NH2" Residue "b ARG 25": "NH1" <-> "NH2" Residue "c ARG 11": "NH1" <-> "NH2" Residue "c ARG 16": "NH1" <-> "NH2" Residue "c ARG 23": "NH1" <-> "NH2" Residue "c ARG 26": "NH1" <-> "NH2" Residue "d ARG 6": "NH1" <-> "NH2" Residue "d GLU 28": "OE1" <-> "OE2" Residue "d ARG 32": "NH1" <-> "NH2" Residue "d GLU 33": "OE1" <-> "OE2" Residue "d ARG 37": "NH1" <-> "NH2" Residue "d ARG 45": "NH1" <-> "NH2" Residue "d PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 61": "OE1" <-> "OE2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "e ARG 41": "NH1" <-> "NH2" Residue "f ARG 6": "NH1" <-> "NH2" Residue "f GLU 7": "OE1" <-> "OE2" Residue "f ARG 9": "NH1" <-> "NH2" Residue "f ARG 23": "NH1" <-> "NH2" Residue "f PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 45": "NH1" <-> "NH2" Residue "f ARG 57": "NH1" <-> "NH2" Residue "f ARG 79": "NH1" <-> "NH2" Residue "h ARG 10": "NH1" <-> "NH2" Residue "h GLU 14": "OE1" <-> "OE2" Residue "h ARG 18": "NH1" <-> "NH2" Residue "h GLU 47": "OE1" <-> "OE2" Residue "h ASP 52": "OD1" <-> "OD2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h ARG 57": "NH1" <-> "NH2" Residue "h TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 131": "OE1" <-> "OE2" Residue "h ARG 137": "NH1" <-> "NH2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "i ARG 55": "NH1" <-> "NH2" Residue "i GLU 56": "OE1" <-> "OE2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "i ARG 77": "NH1" <-> "NH2" Residue "i GLU 85": "OE1" <-> "OE2" Residue "n GLU 42": "OE1" <-> "OE2" Residue "n GLU 78": "OE1" <-> "OE2" Residue "n GLU 85": "OE1" <-> "OE2" Residue "n GLU 89": "OE1" <-> "OE2" Residue "n GLU 90": "OE1" <-> "OE2" Residue "n ASP 103": "OD1" <-> "OD2" Residue "8 GLU 11": "OE1" <-> "OE2" Residue "8 ARG 37": "NH1" <-> "NH2" Residue "8 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 51": "NH1" <-> "NH2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "9 ARG 14": "NH1" <-> "NH2" Residue "9 GLU 46": "OE1" <-> "OE2" Residue "9 ARG 58": "NH1" <-> "NH2" Residue "9 GLU 59": "OE1" <-> "OE2" Residue "9 GLU 69": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 67428 Number of models: 1 Model: "" Number of chains: 102 Chain: "A" Number of atoms: 5269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5269 Classifications: {'peptide': 693} Link IDs: {'PTRANS': 34, 'TRANS': 658} Chain: "B" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3517 Classifications: {'peptide': 455} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 432} Chain: "C" Number of atoms: 3470 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 437, 3465 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 411} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 437, 3465 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 411} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3541 Chain: "G" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1978 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 18, 'TRANS': 220} Chain: "H" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1688 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 18, 'TRANS': 197} Chain: "I" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1519 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 177} Chain: "K" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1395 Classifications: {'peptide': 177} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 162} Chain: "L" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1492 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain breaks: 2 Chain: "j" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 724 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "1" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2716 Classifications: {'peptide': 340} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 325} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3776 Classifications: {'peptide': 469} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 461} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1027 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3815 Classifications: {'peptide': 481} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 466} Chain: "5" Number of atoms: 5197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 5197 Classifications: {'peptide': 654} Link IDs: {'PTRANS': 15, 'TRANS': 638} Chain: "6" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1453 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 622 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 10, 'TRANS': 65} Chain: "D" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 681 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "E" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2806 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain breaks: 1 Chain: "F" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 981 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "J" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1319 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain: "M" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 912 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain: "O" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 543 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "P" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1036 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 648 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 10, 'TRANS': 95} Chain: "U" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1345 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "W" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 974 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 9, 'TRANS': 111} Chain: "X" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain: "Y" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1021 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "Z" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 160} Chain: "a" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1030 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain: "b" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 490 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "c" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 353 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "d" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 751 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "e" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 436 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 6, 'TRANS': 45} Chain: "f" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 642 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "h" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1130 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 10, 'TRANS': 125} Chain: "i" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 646 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "n" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 913 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 9, 'TRANS': 104} Chain: "8" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 594 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "9" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {'PLC': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "S" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "j" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "1" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 205 Unusual residues: {'3PE': 3, 'PLC': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "2" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'CPL': 1, 'T7X': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "3" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'T7X': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'T7X:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'3PE': 3, 'PLC': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "5" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 168 Unusual residues: {'3PE': 3, 'PLC': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Chain: "6" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "g" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 126 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "E" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'3PE': 1, 'CDL': 1, 'NDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 Chain: "J" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 188 Unusual residues: {'3PE': 3, 'LMN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'CDL': 1, 'PLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "X" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 86 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "Z" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 76 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "n" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 92 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 168 Classifications: {'water': 168} Link IDs: {None: 167} Chain: "G" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "L" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "S" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "j" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "1" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "2" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 158 Classifications: {'water': 158} Link IDs: {None: 157} Chain: "3" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "4" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "5" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "6" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "g" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "E" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "M" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "P" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "W" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "Y" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "Z" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "a" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "b" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "d" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "i" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "n" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "9" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 749 SG CYS A 133 128.956 73.332 62.870 1.00 21.62 S ATOM 769 SG CYS A 136 124.912 69.269 59.515 1.00 19.20 S ATOM 809 SG CYS A 142 128.671 66.784 64.064 1.00 21.62 S ATOM 1511 SG CYS A 233 126.757 60.952 57.096 1.00 13.23 S ATOM 1139 SG CYS A 183 131.855 61.579 52.814 1.00 13.36 S ATOM 1187 SG CYS A 189 128.267 56.166 52.928 1.00 12.99 S ATOM 1163 SG CYS A 186 131.639 57.360 58.032 1.00 12.41 S ATOM 255 SG CYS A 69 137.411 54.173 60.803 1.00 10.27 S ATOM 338 SG CYS A 80 138.288 57.270 62.661 1.00 13.02 S ATOM 363 SG CYS A 83 141.280 53.662 66.094 1.00 12.37 S ATOM 465 SG CYS A 97 139.722 51.206 63.853 1.00 14.71 S ATOM 7999 SG CYS B 384 145.691 57.728 55.662 1.00 15.43 S ATOM 8019 SG CYS B 387 148.115 60.427 51.935 1.00 18.21 S ATOM 7980 SG CYS B 381 144.480 55.212 49.598 1.00 19.11 S ATOM 8350 SG CYS B 427 150.217 54.172 52.125 1.00 21.45 S ATOM 15051 SG CYS H 127 157.943 62.997 34.352 1.00 43.34 S ATOM 15085 SG CYS H 132 160.765 64.075 32.572 1.00 46.04 S ATOM 15354 SG CYS H 168 159.613 59.271 37.010 1.00 43.04 S ATOM 15377 SG CYS H 172 162.797 59.804 36.801 1.00 48.74 S ATOM 16979 SG CYS I 172 119.368 87.973 77.248 1.00 21.62 S ATOM 17001 SG CYS I 175 117.967 88.113 71.311 1.00 21.62 S ATOM 16953 SG CYS I 169 113.493 90.374 75.641 1.00 21.62 S ATOM 16726 SG CYS I 140 114.782 83.958 75.473 1.00 21.62 S ATOM 16675 SG CYS I 133 120.878 79.508 64.426 1.00 21.62 S ATOM 16656 SG CYS I 130 115.676 82.842 61.376 1.00 21.62 S ATOM 17031 SG CYS I 179 121.353 85.331 63.810 1.00 21.62 S ATOM 16698 SG CYS I 136 116.658 82.614 67.703 1.00 21.62 S ATOM 17844 SG CYS K 86 110.623 97.119 85.985 1.00 21.62 S ATOM 17838 SG CYS K 85 115.279 94.126 89.398 1.00 21.62 S ATOM 18576 SG CYS K 180 114.187 92.308 83.115 1.00 21.62 S ATOM 18348 SG CYS K 150 110.261 90.594 86.822 1.00 21.62 S ATOM 46767 SG CYS M 97 127.542 84.223 49.253 1.00 15.20 S ATOM 46962 SG CYS M 125 125.181 81.463 50.676 1.00 14.94 S ATOM 46989 SG CYS M 128 123.944 84.816 49.941 1.00 15.77 S Time building chain proxies: 32.75, per 1000 atoms: 0.49 Number of scatterers: 67428 At special positions: 0 Unit cell: (197.112, 197.112, 276.06, 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 1 29.99 Fe 28 26.01 S 311 16.00 P 46 15.00 O 13625 8.00 N 10694 7.00 C 42723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS U 46 " - pdb=" SG CYS U 78 " distance=2.05 Simple disulfide: pdb=" SG CYS U 56 " - pdb=" SG CYS U 68 " distance=2.05 Simple disulfide: pdb=" SG CYS U 90 " - pdb=" SG CYS U 121 " distance=2.03 Simple disulfide: pdb=" SG CYS U 100 " - pdb=" SG CYS U 111 " distance=2.04 Simple disulfide: pdb=" SG CYS d 51 " - pdb=" SG CYS d 63 " distance=2.04 Simple disulfide: pdb=" SG CYS 8 26 " - pdb=" SG CYS 8 57 " distance=2.04 Simple disulfide: pdb=" SG CYS 8 36 " - pdb=" SG CYS 8 47 " distance=2.06 Simple disulfide: pdb=" SG CYS 9 15 " - pdb=" SG CYS 9 47 " distance=2.05 Simple disulfide: pdb=" SG CYS 9 25 " - pdb=" SG CYS 9 37 " distance=2.02 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.99 Conformation dependent library (CDL) restraints added in 8.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 803 " pdb=" FE1 FES A 803 " - pdb=" SG CYS A 69 " pdb=" FE1 FES A 803 " - pdb=" SG CYS A 80 " pdb=" FE2 FES A 803 " - pdb=" SG CYS A 83 " pdb=" FE2 FES A 803 " - pdb=" SG CYS A 97 " pdb=" FES H 301 " pdb=" FE1 FES H 301 " - pdb=" SG CYS H 132 " pdb=" FE1 FES H 301 " - pdb=" SG CYS H 127 " pdb=" FE2 FES H 301 " - pdb=" SG CYS H 168 " pdb=" FE2 FES H 301 " - pdb=" SG CYS H 172 " pdb=" SF4 A 801 " pdb=" FE2 SF4 A 801 " - pdb=" NE2 HIS A 129 " pdb=" FE4 SF4 A 801 " - pdb=" SG CYS A 142 " pdb=" FE1 SF4 A 801 " - pdb=" SG CYS A 133 " pdb=" FE3 SF4 A 801 " - pdb=" SG CYS A 136 " pdb=" SF4 A 802 " pdb=" FE4 SF4 A 802 " - pdb=" SG CYS A 186 " pdb=" FE1 SF4 A 802 " - pdb=" SG CYS A 233 " pdb=" FE2 SF4 A 802 " - pdb=" SG CYS A 183 " pdb=" FE3 SF4 A 802 " - pdb=" SG CYS A 189 " pdb=" SF4 B 501 " pdb=" FE3 SF4 B 501 " - pdb=" SG CYS B 381 " pdb=" FE4 SF4 B 501 " - pdb=" SG CYS B 427 " pdb=" FE1 SF4 B 501 " - pdb=" SG CYS B 384 " pdb=" FE2 SF4 B 501 " - pdb=" SG CYS B 387 " pdb=" SF4 I 301 " pdb=" FE2 SF4 I 301 " - pdb=" SG CYS I 175 " pdb=" FE1 SF4 I 301 " - pdb=" SG CYS I 172 " pdb=" FE3 SF4 I 301 " - pdb=" SG CYS I 169 " pdb=" FE4 SF4 I 301 " - pdb=" SG CYS I 140 " pdb=" FE2 SF4 I 301 " - pdb=" NE2 HIS I 118 " pdb=" SF4 I 302 " pdb=" FE3 SF4 I 302 " - pdb=" SG CYS I 179 " pdb=" FE1 SF4 I 302 " - pdb=" SG CYS I 133 " pdb=" FE4 SF4 I 302 " - pdb=" SG CYS I 136 " pdb=" FE2 SF4 I 302 " - pdb=" SG CYS I 130 " pdb=" SF4 K 301 " pdb=" FE1 SF4 K 301 " - pdb=" SG CYS K 86 " pdb=" FE2 SF4 K 301 " - pdb=" SG CYS K 85 " pdb=" FE3 SF4 K 301 " - pdb=" SG CYS K 180 " pdb=" FE4 SF4 K 301 " - pdb=" SG CYS K 150 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" NE2 HIS M 110 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 128 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 125 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 97 " Number of angles added : 3 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15036 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 345 helices and 33 sheets defined 53.1% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 295 through 304 removed outlier: 5.250A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASP A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLY A 303 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 356 through 368 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 417 through 420 No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 422 through 434 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 469 through 476 Processing helix chain 'A' and resid 486 through 489 No H-bonds generated for 'chain 'A' and resid 486 through 489' Processing helix chain 'A' and resid 492 through 507 removed outlier: 4.573A pdb=" N GLY A 495 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE A 501 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 542 through 544 No H-bonds generated for 'chain 'A' and resid 542 through 544' Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 622 through 632 Processing helix chain 'A' and resid 642 through 652 Processing helix chain 'A' and resid 654 through 656 No H-bonds generated for 'chain 'A' and resid 654 through 656' Processing helix chain 'A' and resid 668 through 675 removed outlier: 3.599A pdb=" N VAL A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 42 through 45 removed outlier: 4.501A pdb=" N TYR B 45 " --> pdb=" O GLN B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 94 through 101 removed outlier: 4.346A pdb=" N MET B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 128 through 135 Processing helix chain 'B' and resid 137 through 150 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 206 through 209 Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 247 through 259 removed outlier: 3.718A pdb=" N ALA B 253 " --> pdb=" O THR B 249 " (cutoff:3.500A) Proline residue: B 254 - end of helix Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 341 through 346 Processing helix chain 'B' and resid 365 through 379 Processing helix chain 'B' and resid 385 through 403 removed outlier: 4.596A pdb=" N THR B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 421 Processing helix chain 'B' and resid 429 through 458 Proline residue: B 436 - end of helix Proline residue: B 446 - end of helix Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 123 through 129 removed outlier: 3.743A pdb=" N GLU C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 141 Proline residue: C 137 - end of helix removed outlier: 3.921A pdb=" N ASP C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 141 " --> pdb=" O PRO C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 162 Processing helix chain 'C' and resid 168 through 197 Processing helix chain 'C' and resid 201 through 221 removed outlier: 3.680A pdb=" N GLU C 209 " --> pdb=" O TRP C 205 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 265 removed outlier: 3.980A pdb=" N GLN C 253 " --> pdb=" O MET C 249 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ASP C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 293 through 299 removed outlier: 4.725A pdb=" N GLY C 298 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 No H-bonds generated for 'chain 'C' and resid 305 through 308' Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 329 through 353 removed outlier: 3.608A pdb=" N ARG C 341 " --> pdb=" O MET C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 374 No H-bonds generated for 'chain 'C' and resid 371 through 374' Processing helix chain 'C' and resid 378 through 389 Processing helix chain 'C' and resid 430 through 442 removed outlier: 4.615A pdb=" N ASP C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N HIS C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 457 Processing helix chain 'C' and resid 461 through 465 Processing helix chain 'G' and resid 36 through 38 No H-bonds generated for 'chain 'G' and resid 36 through 38' Processing helix chain 'G' and resid 42 through 44 No H-bonds generated for 'chain 'G' and resid 42 through 44' Processing helix chain 'G' and resid 60 through 81 removed outlier: 3.623A pdb=" N ARG G 63 " --> pdb=" O PRO G 60 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLN G 66 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 114 removed outlier: 4.679A pdb=" N ILE G 106 " --> pdb=" O SER G 103 " (cutoff:3.500A) Proline residue: G 107 - end of helix Processing helix chain 'G' and resid 173 through 186 removed outlier: 3.991A pdb=" N TRP G 177 " --> pdb=" O GLY G 174 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET G 185 " --> pdb=" O ALA G 182 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR G 186 " --> pdb=" O TYR G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 248 Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'H' and resid 49 through 61 removed outlier: 3.886A pdb=" N LYS H 61 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 81 removed outlier: 4.901A pdb=" N MET H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Proline residue: H 73 - end of helix Processing helix chain 'H' and resid 87 through 96 Processing helix chain 'H' and resid 101 through 110 Processing helix chain 'H' and resid 130 through 135 removed outlier: 3.876A pdb=" N CYS H 135 " --> pdb=" O PRO H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 147 Processing helix chain 'H' and resid 190 through 202 Processing helix chain 'H' and resid 235 through 237 No H-bonds generated for 'chain 'H' and resid 235 through 237' Processing helix chain 'I' and resid 70 through 79 Processing helix chain 'I' and resid 81 through 95 removed outlier: 3.506A pdb=" N GLN I 93 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE I 94 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 139 Processing helix chain 'I' and resid 174 through 178 Processing helix chain 'I' and resid 197 through 200 Processing helix chain 'I' and resid 204 through 228 removed outlier: 5.768A pdb=" N LEU I 216 " --> pdb=" O ASP I 212 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU I 217 " --> pdb=" O LYS I 213 " (cutoff:3.500A) Proline residue: I 227 - end of helix Processing helix chain 'K' and resid 57 through 74 Processing helix chain 'K' and resid 85 through 94 removed outlier: 3.745A pdb=" N GLU K 89 " --> pdb=" O CYS K 85 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER K 94 " --> pdb=" O MET K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 103 Processing helix chain 'K' and resid 111 through 113 No H-bonds generated for 'chain 'K' and resid 111 through 113' Processing helix chain 'K' and resid 125 through 136 Proline residue: K 129 - end of helix Processing helix chain 'K' and resid 149 through 153 Processing helix chain 'K' and resid 155 through 157 No H-bonds generated for 'chain 'K' and resid 155 through 157' Processing helix chain 'K' and resid 167 through 169 No H-bonds generated for 'chain 'K' and resid 167 through 169' Processing helix chain 'K' and resid 184 through 199 Processing helix chain 'K' and resid 204 through 209 Processing helix chain 'L' and resid 3 through 16 Processing helix chain 'L' and resid 22 through 47 Processing helix chain 'L' and resid 50 through 81 removed outlier: 4.013A pdb=" N LEU L 80 " --> pdb=" O SER L 76 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG L 81 " --> pdb=" O TYR L 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 64 removed outlier: 3.742A pdb=" N ALA S 58 " --> pdb=" O GLU S 54 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 98 removed outlier: 4.181A pdb=" N TYR S 98 " --> pdb=" O ILE S 94 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 108 No H-bonds generated for 'chain 'S' and resid 105 through 108' Processing helix chain 'S' and resid 113 through 137 Processing helix chain 'S' and resid 165 through 170 Processing helix chain 'S' and resid 172 through 189 removed outlier: 3.925A pdb=" N ARG S 188 " --> pdb=" O VAL S 184 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU S 189 " --> pdb=" O TYR S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 206 Processing helix chain 'S' and resid 208 through 211 Processing helix chain 'S' and resid 215 through 228 removed outlier: 3.828A pdb=" N ASP S 219 " --> pdb=" O GLU S 215 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA S 220 " --> pdb=" O ASN S 216 " (cutoff:3.500A) Processing helix chain 'S' and resid 234 through 237 No H-bonds generated for 'chain 'S' and resid 234 through 237' Processing helix chain 'S' and resid 239 through 241 No H-bonds generated for 'chain 'S' and resid 239 through 241' Processing helix chain 'j' and resid 30 through 40 Processing helix chain 'j' and resid 42 through 44 No H-bonds generated for 'chain 'j' and resid 42 through 44' Processing helix chain 'j' and resid 50 through 60 Processing helix chain 'j' and resid 62 through 73 Processing helix chain '1' and resid 3 through 34 removed outlier: 3.631A pdb=" N THR 1 23 " --> pdb=" O VAL 1 19 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 44 through 46 No H-bonds generated for 'chain '1' and resid 44 through 46' Processing helix chain '1' and resid 49 through 59 Processing helix chain '1' and resid 70 through 90 Proline residue: 1 77 - end of helix removed outlier: 4.328A pdb=" N TRP 1 88 " --> pdb=" O ALA 1 84 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL 1 89 " --> pdb=" O LEU 1 85 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL 1 90 " --> pdb=" O ILE 1 86 " (cutoff:3.500A) Processing helix chain '1' and resid 105 through 126 removed outlier: 3.810A pdb=" N GLY 1 116 " --> pdb=" O ILE 1 112 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL 1 117 " --> pdb=" O GLY 1 113 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N PHE 1 118 " --> pdb=" O SER 1 114 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLY 1 119 " --> pdb=" O LEU 1 115 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER 1 120 " --> pdb=" O GLY 1 116 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY 1 124 " --> pdb=" O SER 1 120 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP 1 125 " --> pdb=" O LEU 1 121 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 160 removed outlier: 3.760A pdb=" N ILE 1 149 " --> pdb=" O SER 1 145 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE 1 160 " --> pdb=" O ILE 1 156 " (cutoff:3.500A) Processing helix chain '1' and resid 166 through 174 removed outlier: 3.852A pdb=" N GLN 1 173 " --> pdb=" O ILE 1 169 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG 1 174 " --> pdb=" O ILE 1 170 " (cutoff:3.500A) Processing helix chain '1' and resid 178 through 181 No H-bonds generated for 'chain '1' and resid 178 through 181' Processing helix chain '1' and resid 183 through 196 Processing helix chain '1' and resid 204 through 207 No H-bonds generated for 'chain '1' and resid 204 through 207' Processing helix chain '1' and resid 214 through 216 No H-bonds generated for 'chain '1' and resid 214 through 216' Processing helix chain '1' and resid 222 through 246 Processing helix chain '1' and resid 256 through 262 Processing helix chain '1' and resid 268 through 299 Processing helix chain '1' and resid 305 through 314 Processing helix chain '1' and resid 316 through 333 Proline residue: 1 328 - end of helix Processing helix chain '2' and resid 3 through 14 Processing helix chain '2' and resid 18 through 38 removed outlier: 4.728A pdb=" N ARG 2 22 " --> pdb=" O SER 2 19 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU 2 38 " --> pdb=" O VAL 2 35 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 49 removed outlier: 6.326A pdb=" N ASN 2 48 " --> pdb=" O LEU 2 45 " (cutoff:3.500A) Processing helix chain '2' and resid 63 through 84 removed outlier: 3.531A pdb=" N LEU 2 82 " --> pdb=" O VAL 2 78 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR 2 83 " --> pdb=" O ILE 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 91 through 96 Processing helix chain '2' and resid 103 through 118 Processing helix chain '2' and resid 123 through 142 Processing helix chain '2' and resid 148 through 179 Processing helix chain '2' and resid 184 through 186 No H-bonds generated for 'chain '2' and resid 184 through 186' Processing helix chain '2' and resid 189 through 194 Processing helix chain '2' and resid 198 through 212 removed outlier: 3.692A pdb=" N LYS 2 211 " --> pdb=" O GLY 2 207 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE 2 212 " --> pdb=" O LEU 2 208 " (cutoff:3.500A) Processing helix chain '2' and resid 219 through 227 Processing helix chain '2' and resid 230 through 236 removed outlier: 4.067A pdb=" N TYR 2 235 " --> pdb=" O LEU 2 231 " (cutoff:3.500A) Processing helix chain '2' and resid 239 through 251 Processing helix chain '2' and resid 258 through 274 Processing helix chain '2' and resid 281 through 301 removed outlier: 4.001A pdb=" N LEU 2 299 " --> pdb=" O TYR 2 295 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU 2 300 " --> pdb=" O MET 2 296 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU 2 301 " --> pdb=" O MET 2 297 " (cutoff:3.500A) Processing helix chain '2' and resid 306 through 333 removed outlier: 3.623A pdb=" N ILE 2 331 " --> pdb=" O ILE 2 327 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR 2 332 " --> pdb=" O ILE 2 328 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TYR 2 333 " --> pdb=" O PHE 2 329 " (cutoff:3.500A) Processing helix chain '2' and resid 347 through 350 Processing helix chain '2' and resid 353 through 356 No H-bonds generated for 'chain '2' and resid 353 through 356' Processing helix chain '2' and resid 358 through 372 Processing helix chain '2' and resid 378 through 393 removed outlier: 3.512A pdb=" N ASN 2 393 " --> pdb=" O SER 2 389 " (cutoff:3.500A) Processing helix chain '2' and resid 396 through 421 removed outlier: 3.923A pdb=" N LEU 2 411 " --> pdb=" O LEU 2 407 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR 2 412 " --> pdb=" O ILE 2 408 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU 2 416 " --> pdb=" O TYR 2 412 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU 2 417 " --> pdb=" O TYR 2 413 " (cutoff:3.500A) Processing helix chain '2' and resid 437 through 467 removed outlier: 5.652A pdb=" N PHE 2 454 " --> pdb=" O ILE 2 450 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE 2 455 " --> pdb=" O THR 2 451 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N TYR 2 456 " --> pdb=" O PHE 2 452 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN 2 457 " --> pdb=" O GLY 2 453 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N SER 2 458 " --> pdb=" O PHE 2 454 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU 2 459 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL 2 466 " --> pdb=" O ASP 2 462 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 25 Proline residue: 3 12 - end of helix Processing helix chain '3' and resid 54 through 77 removed outlier: 3.854A pdb=" N ALA 3 60 " --> pdb=" O PHE 3 56 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU 3 64 " --> pdb=" O ALA 3 60 " (cutoff:3.500A) Proline residue: 3 65 - end of helix removed outlier: 3.709A pdb=" N LEU 3 73 " --> pdb=" O GLU 3 69 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU 3 74 " --> pdb=" O ILE 3 70 " (cutoff:3.500A) Proline residue: 3 75 - end of helix Processing helix chain '3' and resid 84 through 107 removed outlier: 3.529A pdb=" N GLY 3 101 " --> pdb=" O ILE 3 97 " (cutoff:3.500A) Processing helix chain '4' and resid 7 through 21 Processing helix chain '4' and resid 25 through 44 Processing helix chain '4' and resid 83 through 103 removed outlier: 3.535A pdb=" N PHE 4 88 " --> pdb=" O LEU 4 84 " (cutoff:3.500A) Proline residue: 4 97 - end of helix removed outlier: 4.144A pdb=" N ASN 4 103 " --> pdb=" O THR 4 99 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 130 removed outlier: 3.524A pdb=" N TRP 4 130 " --> pdb=" O LEU 4 126 " (cutoff:3.500A) Processing helix chain '4' and resid 134 through 155 removed outlier: 4.108A pdb=" N THR 4 144 " --> pdb=" O LEU 4 140 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU 4 145 " --> pdb=" O PHE 4 141 " (cutoff:3.500A) Proline residue: 4 146 - end of helix Processing helix chain '4' and resid 160 through 189 removed outlier: 4.130A pdb=" N THR 4 171 " --> pdb=" O VAL 4 167 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE 4 177 " --> pdb=" O SER 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 197 through 199 No H-bonds generated for 'chain '4' and resid 197 through 199' Processing helix chain '4' and resid 204 through 221 removed outlier: 3.709A pdb=" N LEU 4 212 " --> pdb=" O THR 4 208 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY 4 213 " --> pdb=" O ILE 4 209 " (cutoff:3.500A) Processing helix chain '4' and resid 230 through 237 Processing helix chain '4' and resid 240 through 248 Processing helix chain '4' and resid 250 through 261 removed outlier: 4.090A pdb=" N ALA 4 254 " --> pdb=" O ILE 4 250 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU 4 255 " --> pdb=" O LEU 4 251 " (cutoff:3.500A) Processing helix chain '4' and resid 267 through 294 Proline residue: 4 275 - end of helix removed outlier: 3.873A pdb=" N LEU 4 293 " --> pdb=" O SER 4 289 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG 4 294 " --> pdb=" O LEU 4 290 " (cutoff:3.500A) Processing helix chain '4' and resid 298 through 317 removed outlier: 3.529A pdb=" N SER 4 306 " --> pdb=" O ILE 4 302 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE 4 307 " --> pdb=" O ALA 4 303 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER 4 308 " --> pdb=" O TYR 4 304 " (cutoff:3.500A) Processing helix chain '4' and resid 322 through 348 Proline residue: 4 340 - end of helix Processing helix chain '4' and resid 350 through 354 Processing helix chain '4' and resid 359 through 361 No H-bonds generated for 'chain '4' and resid 359 through 361' Processing helix chain '4' and resid 370 through 383 Processing helix chain '4' and resid 390 through 405 Processing helix chain '4' and resid 407 through 432 removed outlier: 4.470A pdb=" N ILE 4 415 " --> pdb=" O GLY 4 411 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N SER 4 416 " --> pdb=" O ILE 4 412 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL 4 417 " --> pdb=" O SER 4 413 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU 4 418 " --> pdb=" O CYS 4 414 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS 4 430 " --> pdb=" O LYS 4 426 " (cutoff:3.500A) Processing helix chain '4' and resid 448 through 466 Processing helix chain '4' and resid 468 through 474 removed outlier: 4.610A pdb=" N ASN 4 473 " --> pdb=" O ILE 4 470 " (cutoff:3.500A) Processing helix chain '4' and resid 478 through 481 No H-bonds generated for 'chain '4' and resid 478 through 481' Processing helix chain '5' and resid 4 through 26 Proline residue: 5 12 - end of helix Proline residue: 5 19 - end of helix removed outlier: 6.345A pdb=" N ARG 5 24 " --> pdb=" O LEU 5 20 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN 5 25 " --> pdb=" O PHE 5 21 " (cutoff:3.500A) Processing helix chain '5' and resid 28 through 55 Processing helix chain '5' and resid 83 through 106 removed outlier: 3.606A pdb=" N ILE 5 104 " --> pdb=" O HIS 5 100 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY 5 105 " --> pdb=" O ILE 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 113 through 132 Processing helix chain '5' and resid 136 through 154 removed outlier: 3.509A pdb=" N GLY 5 147 " --> pdb=" O TRP 5 143 " (cutoff:3.500A) Processing helix chain '5' and resid 161 through 192 Processing helix chain '5' and resid 197 through 206 removed outlier: 5.336A pdb=" N TYR 5 205 " --> pdb=" O PHE 5 201 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU 5 206 " --> pdb=" O ALA 5 202 " (cutoff:3.500A) Processing helix chain '5' and resid 209 through 226 Processing helix chain '5' and resid 235 through 241 removed outlier: 4.255A pdb=" N MET 5 240 " --> pdb=" O LEU 5 236 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU 5 241 " --> pdb=" O THR 5 237 " (cutoff:3.500A) Processing helix chain '5' and resid 244 through 252 removed outlier: 3.640A pdb=" N ALA 5 252 " --> pdb=" O SER 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 255 through 265 removed outlier: 4.403A pdb=" N GLY 5 259 " --> pdb=" O LEU 5 255 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE 5 260 " --> pdb=" O VAL 5 256 " (cutoff:3.500A) Processing helix chain '5' and resid 267 through 272 removed outlier: 4.511A pdb=" N TYR 5 272 " --> pdb=" O ASN 5 268 " (cutoff:3.500A) Processing helix chain '5' and resid 274 through 297 removed outlier: 3.749A pdb=" N CYS 5 297 " --> pdb=" O LEU 5 293 " (cutoff:3.500A) Processing helix chain '5' and resid 301 through 322 Processing helix chain '5' and resid 325 through 351 removed outlier: 3.851A pdb=" N PHE 5 337 " --> pdb=" O LEU 5 333 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE 5 338 " --> pdb=" O GLY 5 334 " (cutoff:3.500A) Processing helix chain '5' and resid 371 through 384 Processing helix chain '5' and resid 391 through 405 removed outlier: 3.702A pdb=" N THR 5 395 " --> pdb=" O THR 5 391 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ILE 5 398 " --> pdb=" O TYR 5 394 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR 5 403 " --> pdb=" O ILE 5 399 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR 5 404 " --> pdb=" O ILE 5 400 " (cutoff:3.500A) Processing helix chain '5' and resid 409 through 437 removed outlier: 3.908A pdb=" N MET 5 430 " --> pdb=" O VAL 5 427 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR 5 434 " --> pdb=" O LYS 5 431 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU 5 435 " --> pdb=" O ILE 5 432 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR 5 436 " --> pdb=" O LEU 5 433 " (cutoff:3.500A) Processing helix chain '5' and resid 445 through 450 Processing helix chain '5' and resid 456 through 480 Proline residue: 5 461 - end of helix removed outlier: 6.239A pdb=" N GLY 5 473 " --> pdb=" O ALA 5 469 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TRP 5 474 " --> pdb=" O MET 5 470 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASP 5 478 " --> pdb=" O TRP 5 474 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE 5 479 " --> pdb=" O ILE 5 475 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR 5 480 " --> pdb=" O LEU 5 476 " (cutoff:3.500A) Processing helix chain '5' and resid 501 through 504 No H-bonds generated for 'chain '5' and resid 501 through 504' Processing helix chain '5' and resid 508 through 531 Proline residue: 5 514 - end of helix Processing helix chain '5' and resid 533 through 536 No H-bonds generated for 'chain '5' and resid 533 through 536' Processing helix chain '5' and resid 541 through 551 Processing helix chain '5' and resid 556 through 563 Processing helix chain '5' and resid 565 through 578 Processing helix chain '5' and resid 583 through 586 No H-bonds generated for 'chain '5' and resid 583 through 586' Processing helix chain '5' and resid 589 through 607 removed outlier: 5.032A pdb=" N SER 5 607 " --> pdb=" O VAL 5 603 " (cutoff:3.500A) Processing helix chain '5' and resid 613 through 637 Processing helix chain '5' and resid 639 through 654 removed outlier: 3.738A pdb=" N ILE 5 643 " --> pdb=" O PHE 5 639 " (cutoff:3.500A) Proline residue: 5 644 - end of helix Processing helix chain '6' and resid 3 through 25 removed outlier: 3.525A pdb=" N TYR 6 7 " --> pdb=" O TYR 6 3 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE 6 9 " --> pdb=" O THR 6 5 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLU 6 10 " --> pdb=" O TYR 6 6 " (cutoff:3.500A) Processing helix chain '6' and resid 29 through 49 Processing helix chain '6' and resid 53 through 62 Processing helix chain '6' and resid 67 through 77 Processing helix chain '6' and resid 87 through 112 removed outlier: 5.878A pdb=" N ARG 6 92 " --> pdb=" O LYS 6 88 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ASP 6 93 " --> pdb=" O SER 6 89 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU 6 94 " --> pdb=" O ASN 6 90 " (cutoff:3.500A) Proline residue: 6 95 - end of helix removed outlier: 5.102A pdb=" N TYR 6 112 " --> pdb=" O GLY 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 118 through 126 removed outlier: 3.991A pdb=" N ALA 6 125 " --> pdb=" O LYS 6 121 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE 6 126 " --> pdb=" O LEU 6 122 " (cutoff:3.500A) Processing helix chain '6' and resid 146 through 155 Processing helix chain '6' and resid 159 through 180 Proline residue: 6 176 - end of helix Processing helix chain 'g' and resid 12 through 22 Processing helix chain 'g' and resid 24 through 50 removed outlier: 3.899A pdb=" N GLY g 36 " --> pdb=" O ILE g 32 " (cutoff:3.500A) Proline residue: g 37 - end of helix Proline residue: g 45 - end of helix Processing helix chain 'D' and resid 5 through 33 Proline residue: D 10 - end of helix Processing helix chain 'D' and resid 44 through 57 Processing helix chain 'D' and resid 72 through 75 Processing helix chain 'E' and resid 64 through 76 removed outlier: 4.126A pdb=" N TYR E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 96 removed outlier: 3.568A pdb=" N ARG E 91 " --> pdb=" O MET E 88 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N HIS E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 178 through 193 Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'E' and resid 238 through 250 Processing helix chain 'E' and resid 252 through 254 No H-bonds generated for 'chain 'E' and resid 252 through 254' Processing helix chain 'E' and resid 269 through 280 Processing helix chain 'E' and resid 291 through 303 removed outlier: 4.315A pdb=" N ALA E 303 " --> pdb=" O LYS E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 318 removed outlier: 4.001A pdb=" N PHE E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 333 Processing helix chain 'E' and resid 340 through 351 removed outlier: 4.781A pdb=" N PHE E 345 " --> pdb=" O PRO E 341 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LYS E 346 " --> pdb=" O ASP E 342 " (cutoff:3.500A) Proline residue: E 350 - end of helix Processing helix chain 'E' and resid 361 through 369 removed outlier: 3.780A pdb=" N ASN E 365 " --> pdb=" O SER E 361 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR E 369 " --> pdb=" O ASN E 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 60 Processing helix chain 'F' and resid 66 through 84 Processing helix chain 'F' and resid 88 through 95 Processing helix chain 'F' and resid 100 through 120 removed outlier: 3.686A pdb=" N GLU F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 50 Processing helix chain 'J' and resid 59 through 62 No H-bonds generated for 'chain 'J' and resid 59 through 62' Processing helix chain 'J' and resid 67 through 89 Processing helix chain 'J' and resid 94 through 112 removed outlier: 3.941A pdb=" N ARG J 111 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR J 112 " --> pdb=" O LEU J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 134 Processing helix chain 'J' and resid 147 through 149 No H-bonds generated for 'chain 'J' and resid 147 through 149' Processing helix chain 'J' and resid 172 through 179 Processing helix chain 'J' and resid 190 through 193 No H-bonds generated for 'chain 'J' and resid 190 through 193' Processing helix chain 'M' and resid 33 through 36 No H-bonds generated for 'chain 'M' and resid 33 through 36' Processing helix chain 'M' and resid 53 through 64 removed outlier: 6.663A pdb=" N VAL M 62 " --> pdb=" O LYS M 58 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARG M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE M 64 " --> pdb=" O ASN M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 71 No H-bonds generated for 'chain 'M' and resid 69 through 71' Processing helix chain 'M' and resid 78 through 84 Processing helix chain 'O' and resid 33 through 41 Processing helix chain 'O' and resid 49 through 51 No H-bonds generated for 'chain 'O' and resid 49 through 51' Processing helix chain 'O' and resid 66 through 80 Processing helix chain 'O' and resid 86 through 91 Processing helix chain 'O' and resid 95 through 101 Processing helix chain 'P' and resid 18 through 42 removed outlier: 3.647A pdb=" N ARG P 24 " --> pdb=" O GLU P 20 " (cutoff:3.500A) Proline residue: P 37 - end of helix Processing helix chain 'P' and resid 49 through 63 removed outlier: 4.205A pdb=" N HIS P 63 " --> pdb=" O GLU P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 87 Processing helix chain 'P' and resid 93 through 99 removed outlier: 3.603A pdb=" N LYS P 98 " --> pdb=" O ALA P 94 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR P 99 " --> pdb=" O GLN P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 103 No H-bonds generated for 'chain 'P' and resid 101 through 103' Processing helix chain 'P' and resid 115 through 120 Processing helix chain 'Q' and resid 52 through 65 Processing helix chain 'Q' and resid 89 through 103 removed outlier: 3.718A pdb=" N VAL Q 93 " --> pdb=" O SER Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 112 No H-bonds generated for 'chain 'Q' and resid 109 through 112' Processing helix chain 'Q' and resid 118 through 126 Processing helix chain 'R' and resid 9 through 29 Processing helix chain 'R' and resid 33 through 49 Processing helix chain 'R' and resid 56 through 73 Processing helix chain 'U' and resid 32 through 60 removed outlier: 5.013A pdb=" N TYR U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE U 41 " --> pdb=" O SER U 37 " (cutoff:3.500A) Proline residue: U 48 - end of helix Processing helix chain 'U' and resid 64 through 67 No H-bonds generated for 'chain 'U' and resid 64 through 67' Processing helix chain 'U' and resid 69 through 89 Processing helix chain 'U' and resid 91 through 103 Processing helix chain 'U' and resid 108 through 110 No H-bonds generated for 'chain 'U' and resid 108 through 110' Processing helix chain 'U' and resid 112 through 126 Processing helix chain 'U' and resid 142 through 144 No H-bonds generated for 'chain 'U' and resid 142 through 144' Processing helix chain 'U' and resid 157 through 169 Processing helix chain 'W' and resid 30 through 95 Proline residue: W 71 - end of helix Processing helix chain 'X' and resid 28 through 33 Processing helix chain 'X' and resid 37 through 60 Proline residue: X 51 - end of helix Processing helix chain 'X' and resid 72 through 98 Processing helix chain 'X' and resid 105 through 121 Processing helix chain 'X' and resid 133 through 143 Processing helix chain 'X' and resid 146 through 149 Processing helix chain 'Y' and resid 42 through 46 Processing helix chain 'Y' and resid 50 through 54 Processing helix chain 'Y' and resid 115 through 124 Processing helix chain 'Y' and resid 144 through 148 Processing helix chain 'Z' and resid 9 through 11 No H-bonds generated for 'chain 'Z' and resid 9 through 11' Processing helix chain 'Z' and resid 20 through 28 Processing helix chain 'Z' and resid 49 through 51 No H-bonds generated for 'chain 'Z' and resid 49 through 51' Processing helix chain 'Z' and resid 53 through 56 Processing helix chain 'Z' and resid 74 through 76 No H-bonds generated for 'chain 'Z' and resid 74 through 76' Processing helix chain 'Z' and resid 91 through 100 Processing helix chain 'Z' and resid 111 through 123 removed outlier: 3.674A pdb=" N THR Z 115 " --> pdb=" O GLY Z 111 " (cutoff:3.500A) Processing helix chain 'Z' and resid 128 through 134 Processing helix chain 'Z' and resid 137 through 143 Processing helix chain 'Z' and resid 167 through 169 No H-bonds generated for 'chain 'Z' and resid 167 through 169' Processing helix chain 'a' and resid 28 through 32 Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 48 through 50 No H-bonds generated for 'chain 'a' and resid 48 through 50' Processing helix chain 'a' and resid 74 through 76 No H-bonds generated for 'chain 'a' and resid 74 through 76' Processing helix chain 'a' and resid 90 through 113 removed outlier: 3.912A pdb=" N TYR a 113 " --> pdb=" O TYR a 109 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 130 Processing helix chain 'b' and resid 3 through 24 Processing helix chain 'b' and resid 33 through 63 removed outlier: 3.660A pdb=" N VAL b 37 " --> pdb=" O PRO b 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 14 through 16 No H-bonds generated for 'chain 'c' and resid 14 through 16' Processing helix chain 'c' and resid 19 through 21 No H-bonds generated for 'chain 'c' and resid 19 through 21' Processing helix chain 'c' and resid 23 through 26 No H-bonds generated for 'chain 'c' and resid 23 through 26' Processing helix chain 'c' and resid 34 through 48 Processing helix chain 'd' and resid 20 through 62 Proline residue: d 57 - end of helix removed outlier: 5.060A pdb=" N PHE d 60 " --> pdb=" O GLY d 56 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU d 61 " --> pdb=" O PRO d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 74 Processing helix chain 'd' and resid 83 through 86 No H-bonds generated for 'chain 'd' and resid 83 through 86' Processing helix chain 'e' and resid 21 through 50 Proline residue: e 47 - end of helix Processing helix chain 'f' and resid 20 through 36 removed outlier: 6.415A pdb=" N GLY f 31 " --> pdb=" O LYS f 27 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ALA f 32 " --> pdb=" O ASN f 28 " (cutoff:3.500A) Processing helix chain 'f' and resid 73 through 84 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 17 through 26 Processing helix chain 'h' and resid 70 through 72 No H-bonds generated for 'chain 'h' and resid 70 through 72' Processing helix chain 'h' and resid 77 through 81 Processing helix chain 'h' and resid 89 through 91 No H-bonds generated for 'chain 'h' and resid 89 through 91' Processing helix chain 'h' and resid 94 through 96 No H-bonds generated for 'chain 'h' and resid 94 through 96' Processing helix chain 'i' and resid 26 through 51 removed outlier: 3.589A pdb=" N LEU i 49 " --> pdb=" O SER i 45 " (cutoff:3.500A) Proline residue: i 50 - end of helix Processing helix chain 'i' and resid 61 through 77 Processing helix chain 'n' and resid 19 through 45 Processing helix chain 'n' and resid 51 through 53 No H-bonds generated for 'chain 'n' and resid 51 through 53' Processing helix chain 'n' and resid 59 through 88 removed outlier: 3.585A pdb=" N ARG n 88 " --> pdb=" O HIS n 84 " (cutoff:3.500A) Processing helix chain 'n' and resid 93 through 96 No H-bonds generated for 'chain 'n' and resid 93 through 96' Processing helix chain '8' and resid 10 through 15 Processing helix chain '8' and resid 20 through 22 No H-bonds generated for 'chain '8' and resid 20 through 22' Processing helix chain '8' and resid 27 through 39 Proline residue: 8 32 - end of helix Processing helix chain '8' and resid 48 through 75 Processing helix chain '9' and resid 16 through 28 Processing helix chain '9' and resid 34 through 49 Proline residue: 9 39 - end of helix Processing helix chain '9' and resid 51 through 65 Processing helix chain '9' and resid 81 through 83 No H-bonds generated for 'chain '9' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'A' and resid 36 through 41 Processing sheet with id= B, first strand: chain 'A' and resid 176 through 178 Processing sheet with id= C, first strand: chain 'A' and resid 203 through 205 Processing sheet with id= D, first strand: chain 'A' and resid 253 through 258 removed outlier: 6.435A pdb=" N LYS A 273 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 313 through 316 removed outlier: 3.723A pdb=" N LYS A 319 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 374 through 376 removed outlier: 7.516A pdb=" N THR A 375 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA A 348 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N MET A 549 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL A 349 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP A 551 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE A 568 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU A 552 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 570 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 585 " --> pdb=" O TYR A 571 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLY A 573 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU A 587 " --> pdb=" O GLY A 573 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 438 through 442 Processing sheet with id= H, first strand: chain 'A' and resid 598 through 600 Processing sheet with id= I, first strand: chain 'B' and resid 242 through 246 removed outlier: 7.009A pdb=" N TYR B 114 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N THR B 245 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B 116 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 155 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL B 117 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TYR B 157 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA B 119 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR B 159 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP B 196 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE B 158 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR B 198 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE B 160 " --> pdb=" O TYR B 198 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS B 200 " --> pdb=" O ILE B 160 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 275 through 277 Processing sheet with id= K, first strand: chain 'B' and resid 280 through 282 removed outlier: 6.242A pdb=" N VAL B 356 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 472 through 474 Processing sheet with id= M, first strand: chain 'C' and resid 83 through 87 removed outlier: 3.524A pdb=" N ARG C 111 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N SER C 105 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 397 through 405 Processing sheet with id= O, first strand: chain 'G' and resid 122 through 130 removed outlier: 6.717A pdb=" N ASN G 143 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE G 126 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL G 141 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA G 128 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLU G 139 " --> pdb=" O ALA G 128 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU G 96 " --> pdb=" O ARG G 152 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR G 158 " --> pdb=" O VAL G 100 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 220 through 225 Processing sheet with id= Q, first strand: chain 'H' and resid 161 through 166 removed outlier: 6.507A pdb=" N TYR H 122 " --> pdb=" O THR H 162 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N SER H 164 " --> pdb=" O TYR H 122 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU H 124 " --> pdb=" O SER H 164 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL H 166 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE H 126 " --> pdb=" O VAL H 166 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 118 through 120 Processing sheet with id= S, first strand: chain 'I' and resid 145 through 151 removed outlier: 6.145A pdb=" N GLU I 150 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N THR I 159 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 78 through 82 removed outlier: 6.337A pdb=" N ILE K 116 " --> pdb=" O VAL K 79 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE K 81 " --> pdb=" O ILE K 116 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE K 118 " --> pdb=" O PHE K 81 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP K 143 " --> pdb=" O MET K 117 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL K 119 " --> pdb=" O TRP K 143 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE K 145 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL K 175 " --> pdb=" O SER K 146 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain '2' and resid 52 through 54 Processing sheet with id= V, first strand: chain '4' and resid 57 through 59 Processing sheet with id= W, first strand: chain '5' and resid 60 through 63 removed outlier: 3.764A pdb=" N ILE 5 60 " --> pdb=" O ILE 5 81 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '5' and resid 66 through 70 removed outlier: 6.584A pdb=" N ILE 5 75 " --> pdb=" O TYR 5 67 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN 5 69 " --> pdb=" O LEU 5 73 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU 5 73 " --> pdb=" O ASN 5 69 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 31 through 33 Processing sheet with id= Z, first strand: chain 'E' and resid 258 through 261 removed outlier: 6.641A pdb=" N ILE E 199 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU E 261 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ARG E 201 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR E 79 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL E 58 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL E 81 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 223 through 225 Processing sheet with id= AB, first strand: chain 'M' and resid 20 through 22 Processing sheet with id= AC, first strand: chain 'M' and resid 88 through 90 Processing sheet with id= AD, first strand: chain 'M' and resid 94 through 97 Processing sheet with id= AE, first strand: chain 'Y' and resid 128 through 131 Processing sheet with id= AF, first strand: chain 'f' and resid 41 through 46 Processing sheet with id= AG, first strand: chain 'h' and resid 59 through 62 removed outlier: 3.665A pdb=" N GLY h 37 " --> pdb=" O PHE h 45 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU h 47 " --> pdb=" O LEU h 35 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU h 35 " --> pdb=" O GLU h 47 " (cutoff:3.500A) 2859 hydrogen bonds defined for protein. 8055 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.94 Time building geometry restraints manager: 25.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 26816 1.39 - 1.62: 39892 1.62 - 1.84: 554 1.84 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 67342 Sorted by residual: bond pdb=" C5N NDP E 400 " pdb=" C6N NDP E 400 " ideal model delta sigma weight residual 1.337 1.548 -0.211 2.40e-02 1.74e+03 7.73e+01 bond pdb=" CZ 2MR C 121 " pdb=" NH1 2MR C 121 " ideal model delta sigma weight residual 1.281 1.439 -0.158 2.00e-02 2.50e+03 6.23e+01 bond pdb=" C1 LMN j 101 " pdb=" O5 LMN j 101 " ideal model delta sigma weight residual 1.403 1.545 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C1 LMN J 202 " pdb=" O5 LMN J 202 " ideal model delta sigma weight residual 1.403 1.544 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C1D NDP E 400 " pdb=" C2D NDP E 400 " ideal model delta sigma weight residual 1.560 1.300 0.260 3.70e-02 7.30e+02 4.94e+01 ... (remaining 67337 not shown) Histogram of bond angle deviations from ideal: 73.47 - 86.66: 76 86.66 - 99.84: 15 99.84 - 113.03: 37975 113.03 - 126.22: 52070 126.22 - 139.41: 1004 Bond angle restraints: 91140 Sorted by residual: angle pdb=" PA NDP E 400 " pdb=" O3 NDP E 400 " pdb=" PN NDP E 400 " ideal model delta sigma weight residual 107.74 125.63 -17.89 1.95e+00 2.62e-01 8.38e+01 angle pdb=" C11 CDL E 402 " pdb=" CA5 CDL E 402 " pdb=" OA6 CDL E 402 " ideal model delta sigma weight residual 111.33 120.99 -9.66 1.32e+00 5.72e-01 5.34e+01 angle pdb=" C51 CDL X 201 " pdb=" CB5 CDL X 201 " pdb=" OB6 CDL X 201 " ideal model delta sigma weight residual 111.33 120.79 -9.46 1.32e+00 5.72e-01 5.12e+01 angle pdb=" C11 CDL n 200 " pdb=" CA5 CDL n 200 " pdb=" OA6 CDL n 200 " ideal model delta sigma weight residual 111.33 120.68 -9.35 1.32e+00 5.72e-01 5.00e+01 angle pdb=" C51 CDL W 402 " pdb=" CB5 CDL W 402 " pdb=" OB6 CDL W 402 " ideal model delta sigma weight residual 111.33 120.66 -9.33 1.32e+00 5.72e-01 4.98e+01 ... (remaining 91135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 38108 33.80 - 67.60: 1767 67.60 - 101.39: 139 101.39 - 135.19: 7 135.19 - 168.99: 3 Dihedral angle restraints: 40024 sinusoidal: 16605 harmonic: 23419 Sorted by residual: dihedral pdb=" CA LEU 5 554 " pdb=" C LEU 5 554 " pdb=" N VAL 5 555 " pdb=" CA VAL 5 555 " ideal model delta harmonic sigma weight residual 180.00 -131.38 -48.62 0 5.00e+00 4.00e-02 9.46e+01 dihedral pdb=" CA ALA U 6 " pdb=" C ALA U 6 " pdb=" N ALA U 7 " pdb=" CA ALA U 7 " ideal model delta harmonic sigma weight residual -180.00 -136.96 -43.04 0 5.00e+00 4.00e-02 7.41e+01 dihedral pdb=" CA TYR C 311 " pdb=" C TYR C 311 " pdb=" N ASP C 312 " pdb=" CA ASP C 312 " ideal model delta harmonic sigma weight residual 180.00 -137.62 -42.38 0 5.00e+00 4.00e-02 7.19e+01 ... (remaining 40021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.973: 10087 0.973 - 1.946: 0 1.946 - 2.918: 0 2.918 - 3.891: 0 3.891 - 4.864: 3 Chirality restraints: 10090 Sorted by residual: chirality pdb=" C1 T7X 2 501 " pdb=" C2 T7X 2 501 " pdb=" C6 T7X 2 501 " pdb=" O1 T7X 2 501 " both_signs ideal model delta sigma weight residual False -2.42 2.45 -4.86 2.00e-01 2.50e+01 5.91e+02 chirality pdb=" C1 T7X 2 503 " pdb=" C2 T7X 2 503 " pdb=" C6 T7X 2 503 " pdb=" O1 T7X 2 503 " both_signs ideal model delta sigma weight residual False -2.42 2.17 -4.59 2.00e-01 2.50e+01 5.26e+02 chirality pdb=" C1 T7X 3 201 " pdb=" C2 T7X 3 201 " pdb=" C6 T7X 3 201 " pdb=" O1 T7X 3 201 " both_signs ideal model delta sigma weight residual False -2.42 2.10 -4.52 2.00e-01 2.50e+01 5.10e+02 ... (remaining 10087 not shown) Planarity restraints: 11376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP E 400 " 0.044 2.00e-02 2.50e+03 7.23e-02 5.23e+01 pdb=" C5N NDP E 400 " -0.089 2.00e-02 2.50e+03 pdb=" C6N NDP E 400 " 0.093 2.00e-02 2.50e+03 pdb=" N1N NDP E 400 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP E 400 " -0.077 2.00e-02 2.50e+03 6.05e-02 4.58e+01 pdb=" C3N NDP E 400 " 0.098 2.00e-02 2.50e+03 pdb=" C4N NDP E 400 " -0.041 2.00e-02 2.50e+03 pdb=" C7N NDP E 400 " -0.012 2.00e-02 2.50e+03 pdb=" N1N NDP E 400 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N FME L 1 " -0.058 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" CA FME L 1 " 0.026 2.00e-02 2.50e+03 pdb=" CN FME L 1 " 0.065 2.00e-02 2.50e+03 pdb=" O1 FME L 1 " -0.032 2.00e-02 2.50e+03 ... (remaining 11373 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 884 2.59 - 3.16: 58454 3.16 - 3.74: 120353 3.74 - 4.32: 169151 4.32 - 4.90: 257908 Nonbonded interactions: 606750 Sorted by model distance: nonbonded pdb=" OE2 GLU A 112 " pdb=" O HOH A 901 " model vdw 2.007 2.440 nonbonded pdb=" OD1 ASP d 89 " pdb=" O HOH d 101 " model vdw 2.017 2.440 nonbonded pdb=" OD2 ASP 2 69 " pdb=" O HOH 2 601 " model vdw 2.034 2.440 nonbonded pdb=" OG SER g 56 " pdb=" OE2 GLU U 139 " model vdw 2.040 2.440 nonbonded pdb=" OE1 GLU 4 395 " pdb=" O HOH 4 601 " model vdw 2.053 2.440 ... (remaining 606745 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 Fe 28 7.16 5 Zn 1 6.06 5 P 46 5.49 5 S 311 5.16 5 C 42723 2.51 5 N 10694 2.21 5 O 13625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 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: 6.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 46.020 Check model and map are aligned: 0.790 Convert atoms to be neutral: 0.460 Process input model: 160.860 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 231.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.008 0.260 67342 Z= 0.512 Angle : 1.062 19.926 91140 Z= 0.513 Chirality : 0.096 4.864 10090 Planarity : 0.006 0.089 11376 Dihedral : 18.065 168.989 24961 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.09), residues: 7944 helix: 0.84 (0.08), residues: 4227 sheet: -0.01 (0.25), residues: 405 loop : -0.58 (0.11), residues: 3312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1423 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1222 time to evaluate : 6.160 Fit side-chains outliers start: 201 outliers final: 87 residues processed: 1382 average time/residue: 1.4218 time to fit residues: 2588.3805 Evaluate side-chains 976 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 889 time to evaluate : 6.129 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 80 residues processed: 8 average time/residue: 0.5118 time to fit residues: 15.6208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 664 optimal weight: 2.9990 chunk 596 optimal weight: 9.9990 chunk 330 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 402 optimal weight: 0.5980 chunk 318 optimal weight: 3.9990 chunk 616 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 375 optimal weight: 8.9990 chunk 459 optimal weight: 3.9990 chunk 714 optimal weight: 7.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 322 ASN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN B 305 HIS B 363 GLN B 370 GLN B 443 ASN C 43 HIS C 91 HIS C 284 GLN ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 HIS G 115 ASN K 137 GLN S 61 GLN S 132 ASN j 24 HIS j 73 GLN 1 310 ASN 2 430 ASN 3 53 ASN 4 103 ASN ** 4 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 HIS D 26 GLN ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 GLN E 331 ASN F 41 ASN F 80 GLN P 58 GLN P 111 GLN P 122 ASN Q 128 GLN R 34 GLN R 93 ASN U 119 ASN U 169 ASN Y 55 ASN Y 135 HIS Y 157 HIS Z 79 HIS a 73 ASN d 16 ASN n 47 HIS 9 40 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 67342 Z= 0.259 Angle : 0.665 13.811 91140 Z= 0.341 Chirality : 0.045 0.327 10090 Planarity : 0.005 0.173 11376 Dihedral : 12.162 170.479 9902 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.77 % Favored : 97.19 % Rotamer Outliers : 5.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.09), residues: 7944 helix: 1.22 (0.08), residues: 4176 sheet: 0.10 (0.26), residues: 382 loop : -0.50 (0.10), residues: 3386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 375 poor density : 946 time to evaluate : 6.117 Fit side-chains revert: symmetry clash outliers start: 375 outliers final: 159 residues processed: 1215 average time/residue: 1.3745 time to fit residues: 2238.3561 Evaluate side-chains 1040 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 881 time to evaluate : 6.214 Switching outliers to nearest non-outliers outliers start: 159 outliers final: 129 residues processed: 33 average time/residue: 0.7350 time to fit residues: 48.2929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 397 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 594 optimal weight: 20.0000 chunk 486 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 715 optimal weight: 9.9990 chunk 773 optimal weight: 0.6980 chunk 637 optimal weight: 9.9990 chunk 710 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 574 optimal weight: 0.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN C 91 HIS C 284 GLN C 372 ASN K 51 GLN K 137 GLN S 132 ASN j 24 HIS j 73 GLN 1 310 ASN 2 252 ASN 2 430 ASN ** 4 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 61 ASN 5 358 GLN D 26 GLN E 331 ASN F 41 ASN F 80 GLN P 58 GLN P 72 GLN Q 128 GLN R 34 GLN R 75 HIS Y 55 ASN Y 135 HIS Z 120 ASN a 73 ASN h 91 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.112 67342 Z= 0.217 Angle : 0.611 11.876 91140 Z= 0.314 Chirality : 0.043 0.250 10090 Planarity : 0.005 0.057 11376 Dihedral : 11.785 177.956 9902 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.31 % Rotamer Outliers : 4.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.78 (0.09), residues: 7944 helix: 1.36 (0.08), residues: 4193 sheet: 0.11 (0.25), residues: 405 loop : -0.45 (0.11), residues: 3346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 928 time to evaluate : 6.227 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 329 outliers final: 174 residues processed: 1183 average time/residue: 1.3753 time to fit residues: 2183.6730 Evaluate side-chains 1047 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 873 time to evaluate : 6.088 Switching outliers to nearest non-outliers outliers start: 174 outliers final: 145 residues processed: 31 average time/residue: 0.7710 time to fit residues: 46.0888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 707 optimal weight: 9.9990 chunk 538 optimal weight: 0.4980 chunk 371 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 341 optimal weight: 10.0000 chunk 480 optimal weight: 9.9990 chunk 718 optimal weight: 20.0000 chunk 760 optimal weight: 8.9990 chunk 375 optimal weight: 5.9990 chunk 680 optimal weight: 9.9990 chunk 205 optimal weight: 0.6980 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN A 718 ASN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN B 363 GLN C 91 HIS C 284 GLN K 100 GLN K 137 GLN K 200 ASN j 11 GLN j 24 HIS j 73 GLN 1 310 ASN 2 29 ASN 2 430 ASN ** 4 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 61 ASN E 331 ASN F 41 ASN F 80 GLN M 27 ASN P 58 GLN R 34 GLN R 75 HIS Y 55 ASN Y 135 HIS Z 91 GLN Z 120 ASN a 65 ASN a 73 ASN c 20 ASN d 16 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 67342 Z= 0.245 Angle : 0.633 12.213 91140 Z= 0.325 Chirality : 0.044 0.251 10090 Planarity : 0.005 0.058 11376 Dihedral : 11.788 179.524 9902 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Rotamer Outliers : 4.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.71 (0.09), residues: 7944 helix: 1.29 (0.08), residues: 4182 sheet: 0.08 (0.26), residues: 391 loop : -0.46 (0.11), residues: 3371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1230 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 908 time to evaluate : 6.226 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 322 outliers final: 184 residues processed: 1156 average time/residue: 1.3672 time to fit residues: 2122.6419 Evaluate side-chains 1042 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 858 time to evaluate : 6.092 Switching outliers to nearest non-outliers outliers start: 184 outliers final: 159 residues processed: 27 average time/residue: 0.6354 time to fit residues: 37.4041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 633 optimal weight: 9.9990 chunk 431 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 566 optimal weight: 6.9990 chunk 313 optimal weight: 2.9990 chunk 649 optimal weight: 20.0000 chunk 525 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 388 optimal weight: 0.6980 chunk 682 optimal weight: 0.8980 chunk 191 optimal weight: 9.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 457 ASN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN C 91 HIS C 284 GLN K 137 GLN j 24 HIS 1 310 ASN 2 173 ASN 2 393 ASN ** 4 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 61 ASN E 331 ASN F 41 ASN F 80 GLN M 85 GLN P 58 GLN R 34 GLN R 75 HIS Y 55 ASN Z 120 ASN a 73 ASN b 55 GLN d 5 GLN d 16 ASN e 11 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 67342 Z= 0.206 Angle : 0.588 12.971 91140 Z= 0.302 Chirality : 0.042 0.223 10090 Planarity : 0.005 0.138 11376 Dihedral : 11.465 176.133 9902 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.24 % Rotamer Outliers : 4.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.09), residues: 7944 helix: 1.42 (0.08), residues: 4186 sheet: 0.16 (0.25), residues: 398 loop : -0.42 (0.11), residues: 3360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 896 time to evaluate : 6.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 300 outliers final: 191 residues processed: 1131 average time/residue: 1.3866 time to fit residues: 2107.9316 Evaluate side-chains 1052 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 861 time to evaluate : 6.226 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 191 outliers final: 164 residues processed: 31 average time/residue: 0.7739 time to fit residues: 46.5462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 255 optimal weight: 8.9990 chunk 685 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 446 optimal weight: 7.9990 chunk 187 optimal weight: 0.8980 chunk 761 optimal weight: 3.9990 chunk 632 optimal weight: 4.9990 chunk 352 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 251 optimal weight: 20.0000 chunk 399 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 272 ASN C 284 GLN H 181 ASN K 100 GLN K 137 GLN j 11 GLN j 24 HIS j 73 GLN 1 310 ASN 3 85 ASN ** 4 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 61 ASN 5 358 GLN E 331 ASN F 41 ASN F 80 GLN M 85 GLN P 58 GLN R 34 GLN R 75 HIS Y 55 ASN Z 120 ASN a 73 ASN b 55 GLN d 5 GLN e 11 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 67342 Z= 0.162 Angle : 0.541 12.180 91140 Z= 0.277 Chirality : 0.040 0.181 10090 Planarity : 0.004 0.068 11376 Dihedral : 11.024 173.480 9902 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.39 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.09), residues: 7944 helix: 1.61 (0.08), residues: 4187 sheet: 0.17 (0.25), residues: 405 loop : -0.33 (0.11), residues: 3352 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 907 time to evaluate : 6.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 274 outliers final: 172 residues processed: 1124 average time/residue: 1.3874 time to fit residues: 2100.6978 Evaluate side-chains 1031 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 859 time to evaluate : 6.146 Switching outliers to nearest non-outliers outliers start: 172 outliers final: 152 residues processed: 23 average time/residue: 0.8978 time to fit residues: 39.4250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 734 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 433 optimal weight: 9.9990 chunk 556 optimal weight: 6.9990 chunk 430 optimal weight: 5.9990 chunk 640 optimal weight: 4.9990 chunk 425 optimal weight: 7.9990 chunk 758 optimal weight: 10.0000 chunk 474 optimal weight: 10.0000 chunk 462 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN A 457 ASN B 272 ASN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN G 115 ASN K 137 GLN j 24 HIS 1 310 ASN 2 29 ASN 2 173 ASN 2 348 ASN 3 85 ASN ** 4 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS F 41 ASN F 80 GLN M 85 GLN P 58 GLN R 75 HIS ** Y 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 120 ASN a 73 ASN b 55 GLN c 20 ASN e 11 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 67342 Z= 0.370 Angle : 0.759 14.370 91140 Z= 0.387 Chirality : 0.049 0.304 10090 Planarity : 0.006 0.080 11376 Dihedral : 12.007 170.227 9902 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Rotamer Outliers : 4.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.42 (0.09), residues: 7944 helix: 1.02 (0.08), residues: 4189 sheet: 0.09 (0.26), residues: 370 loop : -0.57 (0.11), residues: 3385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 880 time to evaluate : 6.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 301 outliers final: 190 residues processed: 1110 average time/residue: 1.4019 time to fit residues: 2091.1019 Evaluate side-chains 1048 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 858 time to evaluate : 6.175 Switching outliers to nearest non-outliers outliers start: 190 outliers final: 156 residues processed: 38 average time/residue: 0.7871 time to fit residues: 55.4011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 469 optimal weight: 9.9990 chunk 302 optimal weight: 0.8980 chunk 453 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 482 optimal weight: 5.9990 chunk 516 optimal weight: 10.0000 chunk 375 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 596 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 457 ASN A 718 ASN B 272 ASN B 363 GLN C 284 GLN G 115 ASN K 137 GLN j 11 GLN j 24 HIS j 73 GLN 1 310 ASN 3 85 ASN ** 4 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 358 GLN D 76 HIS E 331 ASN F 41 ASN F 80 GLN J 24 ASN M 85 GLN P 58 GLN P 111 GLN R 34 GLN R 75 HIS Z 120 ASN a 73 ASN b 55 GLN d 5 GLN d 16 ASN e 11 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 67342 Z= 0.270 Angle : 0.656 13.416 91140 Z= 0.338 Chirality : 0.045 0.227 10090 Planarity : 0.005 0.076 11376 Dihedral : 11.776 170.998 9902 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.10 % Favored : 96.87 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.52 (0.09), residues: 7944 helix: 1.13 (0.08), residues: 4190 sheet: 0.03 (0.25), residues: 398 loop : -0.56 (0.11), residues: 3356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 874 time to evaluate : 6.289 Fit side-chains revert: symmetry clash outliers start: 240 outliers final: 175 residues processed: 1074 average time/residue: 1.4069 time to fit residues: 2040.2623 Evaluate side-chains 1022 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 847 time to evaluate : 6.162 Switching outliers to nearest non-outliers outliers start: 175 outliers final: 158 residues processed: 20 average time/residue: 0.7218 time to fit residues: 32.4094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 690 optimal weight: 1.9990 chunk 726 optimal weight: 8.9990 chunk 663 optimal weight: 6.9990 chunk 706 optimal weight: 0.5980 chunk 425 optimal weight: 0.0020 chunk 307 optimal weight: 0.5980 chunk 555 optimal weight: 0.0370 chunk 216 optimal weight: 6.9990 chunk 638 optimal weight: 3.9990 chunk 668 optimal weight: 7.9990 chunk 704 optimal weight: 9.9990 overall best weight: 0.6468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN A 457 ASN A 718 ASN B 272 ASN C 284 GLN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 11 GLN j 24 HIS j 73 GLN 1 310 ASN 2 227 ASN 3 117 ASN ** 4 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 537 ASN D 33 ASN E 331 ASN F 41 ASN F 80 GLN J 24 ASN M 85 GLN ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN R 34 GLN ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 120 ASN a 73 ASN b 55 GLN d 5 GLN e 11 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 67342 Z= 0.148 Angle : 0.540 11.879 91140 Z= 0.276 Chirality : 0.040 0.190 10090 Planarity : 0.005 0.355 11376 Dihedral : 10.847 173.968 9902 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.53 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.09), residues: 7944 helix: 1.59 (0.08), residues: 4178 sheet: 0.07 (0.25), residues: 411 loop : -0.39 (0.11), residues: 3355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 899 time to evaluate : 6.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 188 outliers final: 147 residues processed: 1072 average time/residue: 1.3849 time to fit residues: 1996.2422 Evaluate side-chains 999 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 852 time to evaluate : 6.379 Switching outliers to nearest non-outliers outliers start: 147 outliers final: 140 residues processed: 8 average time/residue: 0.8023 time to fit residues: 18.1090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 464 optimal weight: 7.9990 chunk 747 optimal weight: 2.9990 chunk 456 optimal weight: 0.0370 chunk 354 optimal weight: 4.9990 chunk 519 optimal weight: 10.0000 chunk 784 optimal weight: 9.9990 chunk 721 optimal weight: 10.0000 chunk 624 optimal weight: 8.9990 chunk 64 optimal weight: 0.0470 chunk 482 optimal weight: 20.0000 chunk 382 optimal weight: 7.9990 overall best weight: 3.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN A 457 ASN A 718 ASN B 272 ASN C 284 GLN K 137 GLN j 11 GLN j 24 HIS 1 310 ASN 2 29 ASN 2 173 ASN 3 117 ASN ** 4 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 537 ASN D 33 ASN D 76 HIS F 41 ASN F 80 GLN M 85 GLN P 58 GLN R 75 HIS Z 120 ASN a 73 ASN b 55 GLN e 11 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 67342 Z= 0.222 Angle : 0.609 12.862 91140 Z= 0.312 Chirality : 0.043 0.206 10090 Planarity : 0.005 0.307 11376 Dihedral : 11.110 173.012 9902 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.09), residues: 7944 helix: 1.47 (0.08), residues: 4182 sheet: 0.21 (0.26), residues: 398 loop : -0.41 (0.11), residues: 3364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15888 Ramachandran restraints generated. 7944 Oldfield, 0 Emsley, 7944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 851 time to evaluate : 6.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 148 residues processed: 1007 average time/residue: 1.3706 time to fit residues: 1861.5909 Evaluate side-chains 978 residues out of total 6878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 830 time to evaluate : 6.130 Switching outliers to nearest non-outliers outliers start: 148 outliers final: 140 residues processed: 9 average time/residue: 0.6728 time to fit residues: 18.2180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 495 optimal weight: 10.0000 chunk 665 optimal weight: 20.0000 chunk 191 optimal weight: 9.9990 chunk 575 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 173 optimal weight: 7.9990 chunk 625 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 642 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN A 718 ASN B 272 ASN C 284 GLN K 137 GLN j 24 HIS 1 310 ASN 2 29 ASN 2 173 ASN ** 4 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 358 GLN 5 537 ASN D 76 HIS E 286 HIS F 41 ASN F 80 GLN M 85 GLN P 58 GLN R 34 GLN R 75 HIS Z 120 ASN a 73 ASN b 55 GLN d 5 GLN e 11 ASN i 78 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121515 restraints weight = 81470.554| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.29 r_work: 0.3210 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 67342 Z= 0.313 Angle : 0.705 14.397 91140 Z= 0.362 Chirality : 0.047 0.244 10090 Planarity : 0.006 0.280 11376 Dihedral : 11.765 170.788 9902 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.70 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.52 (0.09), residues: 7944 helix: 1.12 (0.08), residues: 4179 sheet: 0.10 (0.25), residues: 396 loop : -0.54 (0.11), residues: 3369 =============================================================================== Job complete usr+sys time: 30834.78 seconds wall clock time: 533 minutes 46.22 seconds (32026.22 seconds total)