Starting phenix.real_space_refine (version: dev) on Fri Apr 22 13:11:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzs_4130/04_2022/5lzs_4130_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzs_4130/04_2022/5lzs_4130.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzs_4130/04_2022/5lzs_4130_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzs_4130/04_2022/5lzs_4130_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzs_4130/04_2022/5lzs_4130_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzs_4130/04_2022/5lzs_4130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzs_4130/04_2022/5lzs_4130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzs_4130/04_2022/5lzs_4130_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzs_4130/04_2022/5lzs_4130_updated.pdb" } resolution = 3.31 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= 0.001 sd= 0.018 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 109": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 10": "NH1" <-> "NH2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D ARG 108": "NH1" <-> "NH2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "E GLU 247": "OE1" <-> "OE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "F ARG 235": "NH1" <-> "NH2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "G ARG 142": "NH1" <-> "NH2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G GLU 162": "OE1" <-> "OE2" Residue "G ARG 166": "NH1" <-> "NH2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G ARG 242": "NH1" <-> "NH2" Residue "G GLU 263": "OE1" <-> "OE2" Residue "G GLU 273": "OE1" <-> "OE2" Residue "G ARG 287": "NH1" <-> "NH2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H GLU 44": "OE1" <-> "OE2" Residue "H ARG 89": "NH1" <-> "NH2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H ARG 127": "NH1" <-> "NH2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "I ARG 4": "NH1" <-> "NH2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "I ARG 98": "NH1" <-> "NH2" Residue "I ARG 116": "NH1" <-> "NH2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I ARG 153": "NH1" <-> "NH2" Residue "I ARG 154": "NH1" <-> "NH2" Residue "I ARG 162": "NH1" <-> "NH2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I ARG 203": "NH1" <-> "NH2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J GLU 41": "OE1" <-> "OE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J GLU 93": "OE1" <-> "OE2" Residue "J GLU 111": "OE1" <-> "OE2" Residue "J ARG 146": "NH1" <-> "NH2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "J ARG 164": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 65": "NH1" <-> "NH2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L ARG 102": "NH1" <-> "NH2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "L GLU 119": "OE1" <-> "OE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "L ARG 158": "NH1" <-> "NH2" Residue "L GLU 164": "OE1" <-> "OE2" Residue "L GLU 171": "OE1" <-> "OE2" Residue "L GLU 201": "OE1" <-> "OE2" Residue "M GLU 8": "OE1" <-> "OE2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "M GLU 99": "OE1" <-> "OE2" Residue "M ARG 109": "NH1" <-> "NH2" Residue "M ARG 119": "NH1" <-> "NH2" Residue "M ARG 121": "NH1" <-> "NH2" Residue "M GLU 126": "OE1" <-> "OE2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 189": "NH1" <-> "NH2" Residue "N ARG 194": "NH1" <-> "NH2" Residue "O ARG 78": "NH1" <-> "NH2" Residue "O ARG 128": "NH1" <-> "NH2" Residue "O ARG 140": "NH1" <-> "NH2" Residue "O GLU 144": "OE1" <-> "OE2" Residue "O GLU 157": "OE1" <-> "OE2" Residue "O GLU 158": "OE1" <-> "OE2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P GLU 9": "OE1" <-> "OE2" Residue "P GLU 31": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 115": "OE1" <-> "OE2" Residue "P GLU 147": "OE1" <-> "OE2" Residue "Q GLU 17": "OE1" <-> "OE2" Residue "Q ARG 37": "NH1" <-> "NH2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q GLU 76": "OE1" <-> "OE2" Residue "Q ARG 91": "NH1" <-> "NH2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q ARG 134": "NH1" <-> "NH2" Residue "Q ARG 180": "NH1" <-> "NH2" Residue "Q ARG 181": "NH1" <-> "NH2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R ARG 42": "NH1" <-> "NH2" Residue "R ARG 74": "NH1" <-> "NH2" Residue "R GLU 91": "OE1" <-> "OE2" Residue "R ARG 117": "NH1" <-> "NH2" Residue "R TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R GLU 160": "OE1" <-> "OE2" Residue "R ARG 173": "NH1" <-> "NH2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "S ARG 31": "NH1" <-> "NH2" Residue "S ARG 43": "NH1" <-> "NH2" Residue "S GLU 69": "OE1" <-> "OE2" Residue "S ARG 83": "NH1" <-> "NH2" Residue "S ARG 111": "NH1" <-> "NH2" Residue "S ARG 118": "NH1" <-> "NH2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S ARG 139": "NH1" <-> "NH2" Residue "S ARG 161": "NH1" <-> "NH2" Residue "S ARG 166": "NH1" <-> "NH2" Residue "T GLU 111": "OE1" <-> "OE2" Residue "T GLU 118": "OE1" <-> "OE2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T GLU 137": "OE1" <-> "OE2" Residue "T GLU 149": "OE1" <-> "OE2" Residue "T GLU 152": "OE1" <-> "OE2" Residue "T GLU 157": "OE1" <-> "OE2" Residue "U GLU 40": "OE1" <-> "OE2" Residue "U ARG 65": "NH1" <-> "NH2" Residue "V ARG 6": "NH1" <-> "NH2" Residue "V ARG 48": "NH1" <-> "NH2" Residue "V ARG 51": "NH1" <-> "NH2" Residue "V GLU 71": "OE1" <-> "OE2" Residue "V ARG 85": "NH1" <-> "NH2" Residue "V TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 89": "NH1" <-> "NH2" Residue "V GLU 111": "OE1" <-> "OE2" Residue "V ARG 131": "NH1" <-> "NH2" Residue "W ARG 19": "NH1" <-> "NH2" Residue "W ARG 80": "NH1" <-> "NH2" Residue "W GLU 99": "OE1" <-> "OE2" Residue "X ARG 53": "NH1" <-> "NH2" Residue "X GLU 91": "OE1" <-> "OE2" Residue "X ARG 129": "NH1" <-> "NH2" Residue "X GLU 133": "OE1" <-> "OE2" Residue "X ARG 139": "NH1" <-> "NH2" Residue "Y ARG 27": "NH1" <-> "NH2" Residue "Y GLU 83": "OE1" <-> "OE2" Residue "Y ARG 87": "NH1" <-> "NH2" Residue "Y GLU 120": "OE1" <-> "OE2" Residue "Y GLU 131": "OE1" <-> "OE2" Residue "Z TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 65": "NH1" <-> "NH2" Residue "Z GLU 113": "OE1" <-> "OE2" Residue "Z GLU 119": "OE1" <-> "OE2" Residue "Z GLU 120": "OE1" <-> "OE2" Residue "a ARG 4": "NH1" <-> "NH2" Residue "a ARG 9": "NH1" <-> "NH2" Residue "a ARG 21": "NH1" <-> "NH2" Residue "a ARG 65": "NH1" <-> "NH2" Residue "a GLU 84": "OE1" <-> "OE2" Residue "a ARG 105": "NH1" <-> "NH2" Residue "b ARG 14": "NH1" <-> "NH2" Residue "b ARG 18": "NH1" <-> "NH2" Residue "b ARG 25": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b GLU 70": "OE1" <-> "OE2" Residue "b ARG 95": "NH1" <-> "NH2" Residue "b ARG 109": "NH1" <-> "NH2" Residue "b ARG 111": "NH1" <-> "NH2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "c GLU 59": "OE1" <-> "OE2" Residue "c GLU 61": "OE1" <-> "OE2" Residue "c GLU 80": "OE1" <-> "OE2" Residue "c TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 19": "OE1" <-> "OE2" Residue "d ARG 90": "NH1" <-> "NH2" Residue "d GLU 124": "OE1" <-> "OE2" Residue "e ARG 36": "NH1" <-> "NH2" Residue "e ARG 39": "NH1" <-> "NH2" Residue "e GLU 84": "OE1" <-> "OE2" Residue "e GLU 86": "OE1" <-> "OE2" Residue "e ARG 108": "NH1" <-> "NH2" Residue "e ARG 128": "NH1" <-> "NH2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "f GLU 38": "OE1" <-> "OE2" Residue "f ARG 89": "NH1" <-> "NH2" Residue "g ARG 29": "NH1" <-> "NH2" Residue "g ARG 60": "NH1" <-> "NH2" Residue "g GLU 98": "OE1" <-> "OE2" Residue "h ARG 48": "NH1" <-> "NH2" Residue "h GLU 67": "OE1" <-> "OE2" Residue "h ARG 94": "NH1" <-> "NH2" Residue "h GLU 100": "OE1" <-> "OE2" Residue "i ARG 4": "NH1" <-> "NH2" Residue "i ARG 68": "NH1" <-> "NH2" Residue "i ARG 76": "NH1" <-> "NH2" Residue "j ARG 11": "NH1" <-> "NH2" Residue "j ARG 20": "NH1" <-> "NH2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 56": "NH1" <-> "NH2" Residue "j ARG 72": "NH1" <-> "NH2" Residue "j ARG 79": "NH1" <-> "NH2" Residue "j GLU 80": "OE1" <-> "OE2" Residue "k ARG 3": "NH1" <-> "NH2" Residue "k GLU 6": "OE1" <-> "OE2" Residue "k GLU 7": "OE1" <-> "OE2" Residue "k GLU 54": "OE1" <-> "OE2" Residue "l ARG 8": "NH1" <-> "NH2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 36": "NH1" <-> "NH2" Residue "m GLU 53": "OE1" <-> "OE2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 85": "NH1" <-> "NH2" Residue "n ARG 2": "NH1" <-> "NH2" Residue "n ARG 9": "NH1" <-> "NH2" Residue "n ARG 15": "NH1" <-> "NH2" Residue "n ARG 23": "NH1" <-> "NH2" Residue "o ARG 40": "NH1" <-> "NH2" Residue "o ARG 43": "NH1" <-> "NH2" Residue "o ARG 69": "NH1" <-> "NH2" Residue "o ARG 78": "NH1" <-> "NH2" Residue "o GLU 92": "OE1" <-> "OE2" Residue "p ARG 17": "NH1" <-> "NH2" Residue "p ARG 49": "NH1" <-> "NH2" Residue "p ARG 84": "NH1" <-> "NH2" Residue "r ARG 35": "NH1" <-> "NH2" Residue "r ARG 39": "NH1" <-> "NH2" Residue "r GLU 52": "OE1" <-> "OE2" Residue "r ARG 71": "NH1" <-> "NH2" Residue "r ARG 107": "NH1" <-> "NH2" Residue "r ARG 112": "NH1" <-> "NH2" Residue "r ARG 113": "NH1" <-> "NH2" Residue "s GLU 76": "OE1" <-> "OE2" Residue "s GLU 93": "OE1" <-> "OE2" Residue "s GLU 171": "OE1" <-> "OE2" Residue "t ARG 16": "NH1" <-> "NH2" Residue "t GLU 21": "OE1" <-> "OE2" Residue "t ARG 57": "NH1" <-> "NH2" Residue "t GLU 72": "OE1" <-> "OE2" Residue "t GLU 124": "OE1" <-> "OE2" Residue "AA GLU 12": "OE1" <-> "OE2" Residue "AA GLU 13": "OE1" <-> "OE2" Residue "AA GLU 35": "OE1" <-> "OE2" Residue "AA GLU 69": "OE1" <-> "OE2" Residue "AA GLU 118": "OE1" <-> "OE2" Residue "AA ARG 128": "NH1" <-> "NH2" Residue "AA GLU 192": "OE1" <-> "OE2" Residue "AA GLU 196": "OE1" <-> "OE2" Residue "AA GLU 208": "OE1" <-> "OE2" Residue "AA GLU 209": "OE1" <-> "OE2" Residue "AA GLU 213": "OE1" <-> "OE2" Residue "AA GLU 214": "OE1" <-> "OE2" Residue "BB ARG 51": "NH1" <-> "NH2" Residue "BB GLU 68": "OE1" <-> "OE2" Residue "BB GLU 78": "OE1" <-> "OE2" Residue "BB ARG 82": "NH1" <-> "NH2" Residue "BB ARG 107": "NH1" <-> "NH2" Residue "BB GLU 122": "OE1" <-> "OE2" Residue "BB ARG 136": "NH1" <-> "NH2" Residue "BB ARG 162": "NH1" <-> "NH2" Residue "BB ARG 165": "NH1" <-> "NH2" Residue "BB GLU 170": "OE1" <-> "OE2" Residue "BB ARG 213": "NH1" <-> "NH2" Residue "BB GLU 224": "OE1" <-> "OE2" Residue "CC GLU 59": "OE1" <-> "OE2" Residue "CC ARG 68": "NH1" <-> "NH2" Residue "CC GLU 79": "OE1" <-> "OE2" Residue "CC GLU 80": "OE1" <-> "OE2" Residue "CC GLU 105": "OE1" <-> "OE2" Residue "CC ARG 117": "NH1" <-> "NH2" Residue "CC ARG 123": "NH1" <-> "NH2" Residue "CC GLU 146": "OE1" <-> "OE2" Residue "CC ARG 166": "NH1" <-> "NH2" Residue "CC ARG 167": "NH1" <-> "NH2" Residue "CC ARG 200": "NH1" <-> "NH2" Residue "CC ARG 227": "NH1" <-> "NH2" Residue "CC GLU 258": "OE1" <-> "OE2" Residue "CC GLU 268": "OE1" <-> "OE2" Residue "DD GLU 31": "OE1" <-> "OE2" Residue "DD GLU 38": "OE1" <-> "OE2" Residue "DD GLU 47": "OE1" <-> "OE2" Residue "DD GLU 61": "OE1" <-> "OE2" Residue "DD ARG 67": "NH1" <-> "NH2" Residue "DD GLU 81": "OE1" <-> "OE2" Residue "DD GLU 89": "OE1" <-> "OE2" Residue "DD GLU 103": "OE1" <-> "OE2" Residue "DD GLU 128": "OE1" <-> "OE2" Residue "DD ARG 143": "NH1" <-> "NH2" Residue "DD ARG 146": "NH1" <-> "NH2" Residue "DD GLU 212": "OE1" <-> "OE2" Residue "DD GLU 216": "OE1" <-> "OE2" Residue "DD GLU 225": "OE1" <-> "OE2" Residue "EE ARG 11": "NH1" <-> "NH2" Residue "EE ARG 49": "NH1" <-> "NH2" Residue "EE ARG 68": "NH1" <-> "NH2" Residue "EE ARG 77": "NH1" <-> "NH2" Residue "EE GLU 97": "OE1" <-> "OE2" Residue "EE ARG 108": "NH1" <-> "NH2" Residue "EE GLU 117": "OE1" <-> "OE2" Residue "EE ARG 191": "NH1" <-> "NH2" Residue "EE ARG 198": "NH1" <-> "NH2" Residue "EE GLU 199": "OE1" <-> "OE2" Residue "EE ARG 221": "NH1" <-> "NH2" Residue "EE GLU 250": "OE1" <-> "OE2" Residue "EE ARG 252": "NH1" <-> "NH2" Residue "FF GLU 43": "OE1" <-> "OE2" Residue "FF ARG 55": "NH1" <-> "NH2" Residue "FF ARG 62": "NH1" <-> "NH2" Residue "FF ARG 71": "NH1" <-> "NH2" Residue "FF ARG 81": "NH1" <-> "NH2" Residue "FF GLU 106": "OE1" <-> "OE2" Residue "FF GLU 123": "OE1" <-> "OE2" Residue "FF ARG 127": "NH1" <-> "NH2" Residue "FF ARG 135": "NH1" <-> "NH2" Residue "FF GLU 160": "OE1" <-> "OE2" Residue "FF ARG 164": "NH1" <-> "NH2" Residue "FF GLU 176": "OE1" <-> "OE2" Residue "FF GLU 195": "OE1" <-> "OE2" Residue "FF ARG 198": "NH1" <-> "NH2" Residue "GG GLU 29": "OE1" <-> "OE2" Residue "GG GLU 43": "OE1" <-> "OE2" Residue "GG ARG 72": "NH1" <-> "NH2" Residue "GG ARG 131": "NH1" <-> "NH2" Residue "GG ARG 132": "NH1" <-> "NH2" Residue "GG GLU 150": "OE1" <-> "OE2" Residue "GG ARG 178": "NH1" <-> "NH2" Residue "GG ARG 198": "NH1" <-> "NH2" Residue "GG GLU 204": "OE1" <-> "OE2" Residue "GG ARG 216": "NH1" <-> "NH2" Residue "GG GLU 226": "OE1" <-> "OE2" Residue "GG ARG 231": "NH1" <-> "NH2" Residue "GG ARG 233": "NH1" <-> "NH2" Residue "HH GLU 14": "OE1" <-> "OE2" Residue "HH GLU 31": "OE1" <-> "OE2" Residue "HH ARG 41": "NH1" <-> "NH2" Residue "HH GLU 52": "OE1" <-> "OE2" Residue "HH ARG 81": "NH1" <-> "NH2" Residue "HH GLU 131": "OE1" <-> "OE2" Residue "HH GLU 138": "OE1" <-> "OE2" Residue "HH ARG 143": "NH1" <-> "NH2" Residue "HH GLU 167": "OE1" <-> "OE2" Residue "HH GLU 191": "OE1" <-> "OE2" Residue "II ARG 25": "NH1" <-> "NH2" Residue "II ARG 41": "NH1" <-> "NH2" Residue "II ARG 47": "NH1" <-> "NH2" Residue "II GLU 70": "OE1" <-> "OE2" Residue "II GLU 89": "OE1" <-> "OE2" Residue "II GLU 114": "OE1" <-> "OE2" Residue "II ARG 123": "NH1" <-> "NH2" Residue "II GLU 132": "OE1" <-> "OE2" Residue "II GLU 135": "OE1" <-> "OE2" Residue "II ARG 141": "NH1" <-> "NH2" Residue "II GLU 151": "OE1" <-> "OE2" Residue "II GLU 164": "OE1" <-> "OE2" Residue "II GLU 191": "OE1" <-> "OE2" Residue "II GLU 194": "OE1" <-> "OE2" Residue "II GLU 196": "OE1" <-> "OE2" Residue "JJ ARG 18": "NH1" <-> "NH2" Residue "JJ GLU 21": "OE1" <-> "OE2" Residue "JJ GLU 34": "OE1" <-> "OE2" Residue "JJ ARG 38": "NH1" <-> "NH2" Residue "JJ GLU 42": "OE1" <-> "OE2" Residue "JJ ARG 54": "NH1" <-> "NH2" Residue "JJ GLU 65": "OE1" <-> "OE2" Residue "JJ ARG 69": "NH1" <-> "NH2" Residue "JJ GLU 73": "OE1" <-> "OE2" Residue "JJ ARG 83": "NH1" <-> "NH2" Residue "JJ GLU 89": "OE1" <-> "OE2" Residue "JJ ARG 138": "NH1" <-> "NH2" Residue "KK GLU 13": "OE1" <-> "OE2" Residue "KK GLU 18": "OE1" <-> "OE2" Residue "KK GLU 60": "OE1" <-> "OE2" Residue "KK ARG 65": "NH1" <-> "NH2" Residue "KK GLU 74": "OE1" <-> "OE2" Residue "KK GLU 88": "OE1" <-> "OE2" Residue "KK ARG 95": "NH1" <-> "NH2" Residue "KK ARG 96": "NH1" <-> "NH2" Residue "LL GLU 7": "OE1" <-> "OE2" Residue "LL GLU 49": "OE1" <-> "OE2" Residue "LL ARG 97": "NH1" <-> "NH2" Residue "MM GLU 37": "OE1" <-> "OE2" Residue "MM ARG 45": "NH1" <-> "NH2" Residue "MM GLU 58": "OE1" <-> "OE2" Residue "MM GLU 66": "OE1" <-> "OE2" Residue "MM GLU 71": "OE1" <-> "OE2" Residue "MM GLU 97": "OE1" <-> "OE2" Residue "NN ARG 20": "NH1" <-> "NH2" Residue "NN GLU 103": "OE1" <-> "OE2" Residue "NN ARG 104": "NH1" <-> "NH2" Residue "NN ARG 114": "NH1" <-> "NH2" Residue "NN GLU 119": "OE1" <-> "OE2" Residue "NN ARG 121": "NH1" <-> "NH2" Residue "NN GLU 142": "OE1" <-> "OE2" Residue "OO GLU 25": "OE1" <-> "OE2" Residue "OO GLU 68": "OE1" <-> "OE2" Residue "OO ARG 104": "NH1" <-> "NH2" Residue "OO ARG 117": "NH1" <-> "NH2" Residue "OO ARG 128": "NH1" <-> "NH2" Residue "OO GLU 130": "OE1" <-> "OE2" Residue "OO ARG 141": "NH1" <-> "NH2" Residue "OO ARG 150": "NH1" <-> "NH2" Residue "PP GLU 31": "OE1" <-> "OE2" Residue "PP ARG 42": "NH1" <-> "NH2" Residue "PP ARG 51": "NH1" <-> "NH2" Residue "PP ARG 59": "NH1" <-> "NH2" Residue "PP GLU 66": "OE1" <-> "OE2" Residue "PP GLU 71": "OE1" <-> "OE2" Residue "PP GLU 74": "OE1" <-> "OE2" Residue "PP GLU 106": "OE1" <-> "OE2" Residue "QQ GLU 43": "OE1" <-> "OE2" Residue "QQ GLU 53": "OE1" <-> "OE2" Residue "QQ GLU 61": "OE1" <-> "OE2" Residue "QQ GLU 102": "OE1" <-> "OE2" Residue "QQ GLU 107": "OE1" <-> "OE2" Residue "QQ ARG 126": "NH1" <-> "NH2" Residue "QQ GLU 128": "OE1" <-> "OE2" Residue "QQ ARG 140": "NH1" <-> "NH2" Residue "RR ARG 5": "NH1" <-> "NH2" Residue "RR GLU 18": "OE1" <-> "OE2" Residue "RR GLU 36": "OE1" <-> "OE2" Residue "RR ARG 63": "NH1" <-> "NH2" Residue "RR GLU 77": "OE1" <-> "OE2" Residue "RR ARG 81": "NH1" <-> "NH2" Residue "SS ARG 14": "NH1" <-> "NH2" Residue "SS ARG 39": "NH1" <-> "NH2" Residue "SS ARG 55": "NH1" <-> "NH2" Residue "SS GLU 58": "OE1" <-> "OE2" Residue "SS GLU 63": "OE1" <-> "OE2" Residue "SS ARG 86": "NH1" <-> "NH2" Residue "SS GLU 109": "OE1" <-> "OE2" Residue "SS ARG 121": "NH1" <-> "NH2" Residue "SS ARG 142": "NH1" <-> "NH2" Residue "TT ARG 16": "NH1" <-> "NH2" Residue "TT GLU 32": "OE1" <-> "OE2" Residue "TT GLU 44": "OE1" <-> "OE2" Residue "TT GLU 50": "OE1" <-> "OE2" Residue "TT ARG 62": "NH1" <-> "NH2" Residue "TT ARG 84": "NH1" <-> "NH2" Residue "TT ARG 102": "NH1" <-> "NH2" Residue "TT ARG 121": "NH1" <-> "NH2" Residue "UU ARG 19": "NH1" <-> "NH2" Residue "UU GLU 45": "OE1" <-> "OE2" Residue "UU GLU 72": "OE1" <-> "OE2" Residue "UU ARG 87": "NH1" <-> "NH2" Residue "UU GLU 96": "OE1" <-> "OE2" Residue "UU GLU 107": "OE1" <-> "OE2" Residue "UU GLU 111": "OE1" <-> "OE2" Residue "VV GLU 38": "OE1" <-> "OE2" Residue "WW ARG 36": "NH1" <-> "NH2" Residue "WW GLU 115": "OE1" <-> "OE2" Residue "XX ARG 8": "NH1" <-> "NH2" Residue "XX ARG 17": "NH1" <-> "NH2" Residue "XX ARG 18": "NH1" <-> "NH2" Residue "XX GLU 53": "OE1" <-> "OE2" Residue "XX GLU 58": "OE1" <-> "OE2" Residue "XX ARG 67": "NH1" <-> "NH2" Residue "XX GLU 95": "OE1" <-> "OE2" Residue "XX ARG 107": "NH1" <-> "NH2" Residue "XX GLU 139": "OE1" <-> "OE2" Residue "YY ARG 20": "NH1" <-> "NH2" Residue "YY ARG 61": "NH1" <-> "NH2" Residue "YY GLU 86": "OE1" <-> "OE2" Residue "YY ARG 110": "NH1" <-> "NH2" Residue "ZZ ARG 80": "NH1" <-> "NH2" Residue "ZZ ARG 85": "NH1" <-> "NH2" Residue "aa ARG 10": "NH1" <-> "NH2" Residue "aa GLU 46": "OE1" <-> "OE2" Residue "aa GLU 55": "OE1" <-> "OE2" Residue "aa ARG 85": "NH1" <-> "NH2" Residue "aa ARG 87": "NH1" <-> "NH2" Residue "aa ARG 89": "NH1" <-> "NH2" Residue "aa PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bb GLU 13": "OE1" <-> "OE2" Residue "bb ARG 72": "NH1" <-> "NH2" Residue "bb GLU 75": "OE1" <-> "OE2" Residue "cc ARG 13": "NH1" <-> "NH2" Residue "cc GLU 33": "OE1" <-> "OE2" Residue "cc ARG 40": "NH1" <-> "NH2" Residue "cc ARG 44": "NH1" <-> "NH2" Residue "cc GLU 60": "OE1" <-> "OE2" Residue "cc GLU 62": "OE1" <-> "OE2" Residue "cc GLU 64": "OE1" <-> "OE2" Residue "cc ARG 66": "NH1" <-> "NH2" Residue "cc ARG 67": "NH1" <-> "NH2" Residue "ee ARG 81": "NH1" <-> "NH2" Residue "ee ARG 101": "NH1" <-> "NH2" Residue "ee ARG 104": "NH1" <-> "NH2" Residue "ff TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ff GLU 110": "OE1" <-> "OE2" Residue "ff GLU 125": "OE1" <-> "OE2" Residue "ff ARG 138": "NH1" <-> "NH2" Residue "gg ARG 47": "NH1" <-> "NH2" Residue "gg ARG 60": "NH1" <-> "NH2" Residue "gg ARG 100": "NH1" <-> "NH2" Residue "gg PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "gg GLU 273": "OE1" <-> "OE2" Residue "gg GLU 282": "OE1" <-> "OE2" Residue "jj GLU 40": "OE1" <-> "OE2" Residue "jj GLU 43": "OE1" <-> "OE2" Residue "jj GLU 68": "OE1" <-> "OE2" Residue "jj GLU 122": "OE1" <-> "OE2" Residue "jj ARG 134": "NH1" <-> "NH2" Residue "jj GLU 173": "OE1" <-> "OE2" Residue "jj GLU 203": "OE1" <-> "OE2" Residue "jj GLU 293": "OE1" <-> "OE2" Residue "jj GLU 374": "OE1" <-> "OE2" Residue "jj GLU 377": "OE1" <-> "OE2" Residue "jj ARG 382": "NH1" <-> "NH2" Residue "jj GLU 413": "OE1" <-> "OE2" Residue "jj ARG 423": "NH1" <-> "NH2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 220934 Number of models: 1 Model: "" Number of chains: 105 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1898 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 14, 'TRANS': 233} Chain: "B" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3172 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain: "C" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2883 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "D" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2391 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain: "E" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1729 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain breaks: 3 Chain: "F" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1875 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "G" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1879 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain breaks: 1 Chain: "H" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1516 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "I" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1664 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain breaks: 1 Chain: "J" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1362 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "L" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1702 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "M" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1137 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "N" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "O" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1630 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "P" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "Q" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1515 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "R" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1508 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain: "S" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1462 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "T" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "U" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 809 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "V" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1034 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain: "W" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 860 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "X" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "Y" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "Z" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "a" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "b" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 1 Chain: "c" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 761 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "d" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "e" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "f" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "g" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "h" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1013 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "i" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 830 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "j" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "k" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "l" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 447 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "m" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "o" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "r" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "s" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1507 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "t" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1160 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "2" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1616 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna3p_pur': 32, 'rna2p_pyr': 4, 'rna3p_pyr': 33} Link IDs: {'rna3p': 64, 'rna2p': 11} Chain breaks: 3 Chain: "3" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1593 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna3p_pur': 29, 'rna2p_pyr': 7, 'rna3p_pyr': 31} Link IDs: {'rna3p': 60, 'rna2p': 14} Chain breaks: 2 Chain: "5" Number of atoms: 75972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3543, 75972 Classifications: {'RNA': 3543} Modifications used: {'rna3p_pyr': 1387, 'rna2p_pur': 352, 'rna3p_pur': 1594, 'rna2p_pyr': 210} Link IDs: {'rna3p': 2980, 'rna2p': 562} Chain breaks: 30 Chain: "7" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2538 Classifications: {'RNA': 119} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna3p_pur': 55, 'rna2p_pyr': 6, 'rna3p_pyr': 52} Link IDs: {'rna3p': 106, 'rna2p': 12} Chain: "8" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3208 Classifications: {'RNA': 151} Modifications used: {'rna3p_pyr': 63, 'rna2p_pur': 14, 'rna3p_pur': 59, 'rna2p_pyr': 15, '5*END': 1} Link IDs: {'rna3p': 122, 'rna2p': 28} Chain breaks: 1 Chain: "9" Number of atoms: 36229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36229 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 141, 'rna3p_pur': 757, 'rna2p_pyr': 108, 'rna3p_pyr': 691} Link IDs: {'rna3p': 1448, 'rna2p': 248} Chain breaks: 18 Chain: "AA" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "BB" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "CC" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "DD" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "EE" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "FF" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1471 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain breaks: 1 Chain: "GG" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "HH" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "II" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "JJ" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "KK" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "LL" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1175 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 1 Chain: "MM" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "NN" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "OO" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "PP" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1058 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "QQ" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135, 'PCIS': 1} Chain: "RR" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "SS" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "TT" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "UU" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "VV" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "WW" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 125, 'PCIS': 1} Chain: "XX" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "YY" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "ZZ" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "aa" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "bb" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "cc" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 488 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "dd" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "ee" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "ff" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "gg" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "hh" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 210 Classifications: {'RNA': 10} Modifications used: {'rna3p_pyr': 5, 'rna3p_pur': 4, 'rna2p_pyr': 1} Link IDs: {'rna3p': 8, 'rna2p': 1} Chain: "ii" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1616 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna3p_pur': 31, 'rna2p_pyr': 3, 'rna3p_pyr': 34} Link IDs: {'rna3p': 65, 'rna2p': 10} Chain breaks: 1 Chain: "jj" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3383 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 24, 'TRANS': 415, 'PCIS': 1} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 185 Unusual residues: {' MG': 185} Classifications: {'undetermined': 185} Link IDs: {None: 184} Chain: "7" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "8" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "9" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Unusual residues: {' MG': 69} Classifications: {'undetermined': 69} Link IDs: {None: 68} Chain: "aa" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "dd" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "ff" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "jj" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'GDP': 1, ' MG': 1, '7C4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 45410 SG CYS g 46 174.604 168.497 207.344 1.00 84.29 S ATOM 45427 SG CYS g 49 174.506 172.276 206.131 1.00111.11 S ATOM 45690 SG CYS g 83 176.353 171.821 209.150 1.00 81.31 S ATOM 45710 SG CYS g 86 172.934 170.922 209.047 1.00 96.26 S ATOM 47933 SG CYS j 19 202.509 122.680 185.090 1.00 41.12 S ATOM 47961 SG CYS j 22 203.555 120.478 182.764 1.00 38.90 S ATOM 48052 SG CYS j 34 200.691 122.109 181.873 1.00 37.31 S ATOM 48071 SG CYS j 37 200.428 119.155 184.837 1.00 42.39 S ATOM 49676 SG CYS m 70 182.606 138.809 72.844 1.00 56.02 S ATOM 49702 SG CYS m 73 185.800 139.884 74.252 1.00 46.62 S ATOM 49792 SG CYS m 84 186.000 138.537 70.963 1.00 56.37 S ATOM 49836 SG CYS m 89 185.281 136.042 73.696 1.00 52.05 S ATOM 50273 SG CYS o 12 136.169 67.581 145.045 1.00 59.56 S ATOM 50297 SG CYS o 15 134.333 64.810 146.177 1.00 82.55 S ATOM 50766 SG CYS o 72 132.986 68.995 145.316 1.00 76.34 S ATOM 50803 SG CYS o 77 135.513 67.053 148.727 1.00107.25 S ATOM 51333 SG CYS p 39 162.208 174.075 196.779 1.00 54.88 S ATOM 51356 SG CYS p 42 163.511 177.234 197.674 1.00 62.67 S ATOM 51478 SG CYS p 57 165.568 174.671 195.907 1.00 55.11 S ATOM 51494 SG CYS p 60 164.335 174.452 199.439 1.00 67.18 S ATOM A2CLW SG CYSaa 23 110.300 161.274 163.588 1.00 64.96 S ATOM A2CMH SG CYSaa 26 111.589 159.055 159.471 1.00 90.09 S ATOM A2CX4 SG CYSaa 74 110.743 163.716 160.553 1.00 58.96 S ATOM A2CXN SG CYSaa 77 109.082 160.881 160.013 1.00 57.96 S ATOM A2E3T SG CYSdd 21 71.884 167.484 97.054 1.00 71.53 S ATOM A2E4H SG CYSdd 24 75.238 169.767 97.956 1.00 61.25 S ATOM A2E7U SG CYSdd 39 74.233 167.132 99.694 1.00 84.36 S ATOM A2E8K SG CYSdd 42 73.032 170.690 99.920 1.00 74.96 S ATOM A2EXV SG CYSff 121 69.685 162.259 47.641 1.00243.35 S ATOM A2F25 SG CYSff 141 72.641 163.588 49.150 1.00212.76 S ATOM A2F2O SG CYSff 144 70.229 162.043 51.264 1.00221.96 S Time building chain proxies: 81.81, per 1000 atoms: 0.37 Number of scatterers: 220934 At special positions: 0 Unit cell: (291.2, 297.44, 276.64, 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 8 29.99 S 442 16.00 P 5744 15.00 Mg 276 11.99 O 56788 8.00 N 41128 7.00 C 116548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 74.34 Conformation dependent library (CDL) restraints added in 12.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 49 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 86 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 46 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 83 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb=" ZN m 200 " pdb="ZN ZN m 200 " - pdb=" SG CYS m 73 " pdb="ZN ZN m 200 " - pdb=" SG CYS m 89 " pdb="ZN ZN m 200 " - pdb=" SG CYS m 70 " pdb="ZN ZN m 200 " - pdb=" SG CYS m 84 " pdb=" ZN o 200 " pdb="ZN ZN o 200 " - pdb=" SG CYS o 77 " pdb="ZN ZN o 200 " - pdb=" SG CYS o 15 " pdb="ZN ZN o 200 " - pdb=" SG CYS o 12 " pdb="ZN ZN o 200 " - pdb=" SG CYS o 72 " pdb=" ZN p 100 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 57 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 60 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 39 " pdb=" ZNaa 202 " pdb="ZN ZNaa 202 " - pdb=" SG CYSaa 77 " pdb="ZN ZNaa 202 " - pdb=" SG CYSaa 74 " pdb="ZN ZNaa 202 " - pdb=" SG CYSaa 23 " pdb="ZN ZNaa 202 " - pdb=" SG CYSaa 26 " pdb=" ZNdd 100 " pdb="ZN ZNdd 100 " - pdb=" SG CYSdd 39 " pdb="ZN ZNdd 100 " - pdb=" SG CYSdd 21 " pdb="ZN ZNdd 100 " - pdb=" SG CYSdd 24 " pdb="ZN ZNdd 100 " - pdb=" SG CYSdd 42 " pdb=" ZNff 200 " pdb="ZN ZNff 200 " - pdb=" SG CYSff 144 " pdb="ZN ZNff 200 " - pdb=" SG CYSff 141 " pdb="ZN ZNff 200 " - pdb=" SG CYSff 121 " Number of angles added : 42 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22568 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 410 helices and 134 sheets defined 41.2% alpha, 15.9% beta 1741 base pairs and 3017 stacking pairs defined. Time for finding SS restraints: 89.89 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 4.261A pdb=" N GLY A 11 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.585A pdb=" N MET A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.619A pdb=" N ALA A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.755A pdb=" N MET A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'B' and resid 13 through 18 removed outlier: 4.133A pdb=" N LEU B 17 " --> pdb=" O SER B 13 " (cutoff:3.500A) Proline residue: B 18 - end of helix No H-bonds generated for 'chain 'B' and resid 13 through 18' Processing helix chain 'B' and resid 111 through 120 removed outlier: 4.306A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE B 118 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.919A pdb=" N LYS B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TRP B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN B 138 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 157 removed outlier: 3.552A pdb=" N CYS B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 removed outlier: 4.051A pdb=" N LEU B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Proline residue: B 172 - end of helix No H-bonds generated for 'chain 'B' and resid 167 through 172' Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.933A pdb=" N VAL B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.505A pdb=" N LEU B 360 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 356 through 361' Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'C' and resid 25 through 31 removed outlier: 4.348A pdb=" N LYS C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 33 through 49 removed outlier: 3.564A pdb=" N PHE C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ARG C 49 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 134 removed outlier: 3.543A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Proline residue: C 134 - end of helix Processing helix chain 'C' and resid 135 through 141 Processing helix chain 'C' and resid 156 through 161 removed outlier: 4.337A pdb=" N GLY C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 161' Processing helix chain 'C' and resid 163 through 175 removed outlier: 3.507A pdb=" N LYS C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.634A pdb=" N ILE C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.905A pdb=" N ARG C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 193 through 198' Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 253 through 264 removed outlier: 4.363A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.777A pdb=" N ILE C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 302 removed outlier: 3.629A pdb=" N ARG C 300 " --> pdb=" O PRO C 296 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 296 through 302' Processing helix chain 'C' and resid 317 through 322 removed outlier: 4.680A pdb=" N LEU C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 329 Processing helix chain 'C' and resid 330 through 363 removed outlier: 3.919A pdb=" N THR C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR C 339 " --> pdb=" O MET C 335 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG C 342 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLN C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 removed outlier: 5.676A pdb=" N GLN C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR C 62 " --> pdb=" O GLY C 59 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N SER C 63 " --> pdb=" O HIS C 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 58 through 63' Processing helix chain 'D' and resid 9 through 16 removed outlier: 3.527A pdb=" N PHE D 13 " --> pdb=" O ASN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 26 Processing helix chain 'D' and resid 29 through 37 removed outlier: 3.708A pdb=" N LYS D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 4.428A pdb=" N LEU D 83 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 114 Processing helix chain 'D' and resid 115 through 120 removed outlier: 4.863A pdb=" N TYR D 119 " --> pdb=" O MET D 115 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 115 through 120' Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.568A pdb=" N GLY D 161 " --> pdb=" O ASN D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.645A pdb=" N HIS D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS D 198 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 215 removed outlier: 3.609A pdb=" N TYR D 207 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 232 through 251 removed outlier: 4.894A pdb=" N GLU D 237 " --> pdb=" O PRO D 233 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Proline residue: D 251 - end of helix Processing helix chain 'D' and resid 272 through 295 Processing helix chain 'E' and resid 60 through 69 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.065A pdb=" N VAL E 197 " --> pdb=" O HIS E 193 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE E 198 " --> pdb=" O GLN E 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 193 through 198' Processing helix chain 'E' and resid 216 through 222 removed outlier: 3.813A pdb=" N PHE E 220 " --> pdb=" O THR E 216 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS E 221 " --> pdb=" O ASP E 217 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LYS E 222 " --> pdb=" O ALA E 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 216 through 222' Processing helix chain 'E' and resid 246 through 268 removed outlier: 3.516A pdb=" N LYS E 250 " --> pdb=" O THR E 246 " (cutoff:3.500A) Proline residue: E 262 - end of helix Proline residue: E 268 - end of helix Processing helix chain 'E' and resid 269 through 277 removed outlier: 4.836A pdb=" N VAL E 277 " --> pdb=" O TYR E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 290 removed outlier: 5.248A pdb=" N VAL E 290 " --> pdb=" O PRO E 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 78 removed outlier: 4.363A pdb=" N LYS F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU F 67 " --> pdb=" O MET F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 112 Processing helix chain 'F' and resid 125 through 136 Processing helix chain 'F' and resid 145 through 155 removed outlier: 3.904A pdb=" N LYS F 155 " --> pdb=" O GLU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 178 removed outlier: 3.853A pdb=" N ILE F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER F 177 " --> pdb=" O LEU F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 196 Processing helix chain 'F' and resid 199 through 208 removed outlier: 4.944A pdb=" N TRP F 208 " --> pdb=" O ASN F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 247 removed outlier: 3.649A pdb=" N LEU F 242 " --> pdb=" O GLN F 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 127 removed outlier: 3.608A pdb=" N ALA G 121 " --> pdb=" O GLN G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 139 removed outlier: 4.964A pdb=" N PHE G 136 " --> pdb=" O ALA G 132 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN G 138 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL G 139 " --> pdb=" O GLN G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 156 removed outlier: 3.553A pdb=" N LYS G 154 " --> pdb=" O LYS G 150 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 176 Processing helix chain 'G' and resid 192 through 203 removed outlier: 3.690A pdb=" N THR G 198 " --> pdb=" O ASN G 194 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS G 203 " --> pdb=" O LEU G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 239 through 248 removed outlier: 3.835A pdb=" N LEU G 246 " --> pdb=" O ARG G 242 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL G 247 " --> pdb=" O LEU G 243 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N HIS G 248 " --> pdb=" O GLY G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 279 removed outlier: 4.759A pdb=" N GLY G 266 " --> pdb=" O SER G 262 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA G 267 " --> pdb=" O GLU G 263 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU G 268 " --> pdb=" O ASP G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 290 removed outlier: 3.534A pdb=" N ILE G 286 " --> pdb=" O ARG G 282 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N TRP G 290 " --> pdb=" O ILE G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 319 Processing helix chain 'H' and resid 63 through 86 removed outlier: 3.527A pdb=" N ALA H 68 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR H 69 " --> pdb=" O LYS H 65 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE H 73 " --> pdb=" O THR H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 166 removed outlier: 3.538A pdb=" N ASN H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR H 165 " --> pdb=" O ILE H 161 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 3.814A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 10 removed outlier: 4.318A pdb=" N TYR I 9 " --> pdb=" O PRO I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 47 removed outlier: 4.453A pdb=" N PHE I 46 " --> pdb=" O LYS I 42 " (cutoff:3.500A) Proline residue: I 47 - end of helix No H-bonds generated for 'chain 'I' and resid 42 through 47' Processing helix chain 'I' and resid 61 through 80 Processing helix chain 'I' and resid 144 through 160 removed outlier: 3.733A pdb=" N VAL I 148 " --> pdb=" O ASN I 144 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS I 158 " --> pdb=" O ARG I 154 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE I 159 " --> pdb=" O ALA I 155 " (cutoff:3.500A) Proline residue: I 160 - end of helix Processing helix chain 'I' and resid 177 through 188 removed outlier: 4.528A pdb=" N GLU I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 214 removed outlier: 3.984A pdb=" N TRP I 209 " --> pdb=" O PRO I 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 45 removed outlier: 3.503A pdb=" N ARG J 35 " --> pdb=" O ASP J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 91 Processing helix chain 'J' and resid 139 through 144 removed outlier: 4.767A pdb=" N ASP J 143 " --> pdb=" O PHE J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 170 Processing helix chain 'J' and resid 111 through 116 removed outlier: 3.518A pdb=" N ASP J 114 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY J 116 " --> pdb=" O ILE J 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 22 removed outlier: 4.235A pdb=" N ARG L 21 " --> pdb=" O ASP L 17 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL L 22 " --> pdb=" O TRP L 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 17 through 22' Processing helix chain 'L' and resid 27 through 47 removed outlier: 3.777A pdb=" N ALA L 47 " --> pdb=" O ALA L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 Processing helix chain 'L' and resid 87 through 95 removed outlier: 4.272A pdb=" N THR L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY L 95 " --> pdb=" O ALA L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 124 removed outlier: 4.001A pdb=" N LEU L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 147 Processing helix chain 'L' and resid 170 through 176 Processing helix chain 'L' and resid 177 through 192 Processing helix chain 'L' and resid 193 through 211 Processing helix chain 'M' and resid 51 through 56 removed outlier: 3.628A pdb=" N MET M 55 " --> pdb=" O PRO M 51 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLN M 56 " --> pdb=" O PHE M 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 51 through 56' Processing helix chain 'M' and resid 69 through 81 removed outlier: 3.584A pdb=" N VAL M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 90 removed outlier: 5.274A pdb=" N ARG M 90 " --> pdb=" O TRP M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 104 Processing helix chain 'M' and resid 106 through 139 Processing helix chain 'N' and resid 2 through 14 removed outlier: 3.680A pdb=" N TYR N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 3.645A pdb=" N LEU N 33 " --> pdb=" O GLN N 29 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 83 through 88 removed outlier: 3.626A pdb=" N HIS N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY N 88 " --> pdb=" O PRO N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 83 through 88' Processing helix chain 'N' and resid 97 through 111 Processing helix chain 'N' and resid 139 through 146 removed outlier: 4.470A pdb=" N ASN N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) Proline residue: N 146 - end of helix Processing helix chain 'N' and resid 147 through 153 removed outlier: 6.491A pdb=" N ILE N 151 " --> pdb=" O ASP N 147 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR N 152 " --> pdb=" O THR N 148 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS N 153 " --> pdb=" O GLN N 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 147 through 153' Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 165 through 173 removed outlier: 3.550A pdb=" N SER N 171 " --> pdb=" O ALA N 167 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG N 172 " --> pdb=" O GLY N 168 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY N 173 " --> pdb=" O ARG N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 197 Processing helix chain 'O' and resid 15 through 30 removed outlier: 3.625A pdb=" N ILE O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN O 26 " --> pdb=" O ILE O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 42 removed outlier: 3.870A pdb=" N ILE O 41 " --> pdb=" O ARG O 37 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASN O 42 " --> pdb=" O CYS O 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 37 through 42' Processing helix chain 'O' and resid 46 through 61 removed outlier: 3.521A pdb=" N TYR O 54 " --> pdb=" O ASN O 50 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ARG O 61 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 3.813A pdb=" N GLY O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) Proline residue: O 70 - end of helix No H-bonds generated for 'chain 'O' and resid 65 through 70' Processing helix chain 'O' and resid 75 through 89 removed outlier: 3.524A pdb=" N LEU O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) Proline residue: O 89 - end of helix Processing helix chain 'O' and resid 92 through 103 removed outlier: 5.188A pdb=" N LYS O 103 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 116 removed outlier: 4.353A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LYS O 116 " --> pdb=" O TYR O 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 110 through 116' Processing helix chain 'O' and resid 137 through 146 Processing helix chain 'O' and resid 150 through 190 removed outlier: 3.559A pdb=" N ILE O 166 " --> pdb=" O GLU O 162 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LYS O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS O 188 " --> pdb=" O ASN O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 200 Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 54 Processing helix chain 'P' and resid 70 through 77 removed outlier: 4.341A pdb=" N LYS P 74 " --> pdb=" O CYS P 70 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TRP P 76 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'Q' and resid 22 through 39 removed outlier: 3.633A pdb=" N PHE Q 34 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 54 removed outlier: 4.236A pdb=" N GLN Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 72 removed outlier: 3.609A pdb=" N LYS Q 69 " --> pdb=" O ARG Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 117 Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'Q' and resid 146 through 153 removed outlier: 4.318A pdb=" N ARG Q 150 " --> pdb=" O ARG Q 146 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N HIS Q 151 " --> pdb=" O GLU Q 147 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE Q 152 " --> pdb=" O VAL Q 148 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLY Q 153 " --> pdb=" O TYR Q 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 146 through 153' Processing helix chain 'Q' and resid 171 through 176 removed outlier: 5.455A pdb=" N GLU Q 175 " --> pdb=" O GLY Q 171 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG Q 176 " --> pdb=" O ARG Q 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 171 through 176' Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 23 removed outlier: 3.585A pdb=" N VAL R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TRP R 23 " --> pdb=" O LYS R 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 18 through 23' Processing helix chain 'R' and resid 28 through 36 removed outlier: 3.783A pdb=" N ILE R 32 " --> pdb=" O GLU R 28 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASN R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 77 through 82 removed outlier: 3.837A pdb=" N ARG R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LYS R 82 " --> pdb=" O ILE R 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 77 through 82' Processing helix chain 'R' and resid 84 through 113 Proline residue: R 90 - end of helix removed outlier: 6.743A pdb=" N VAL R 93 " --> pdb=" O MET R 89 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG R 104 " --> pdb=" O ARG R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 130 Processing helix chain 'R' and resid 134 through 181 removed outlier: 3.647A pdb=" N LEU R 138 " --> pdb=" O ASN R 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 52 Processing helix chain 'S' and resid 101 through 117 Processing helix chain 'S' and resid 120 through 125 removed outlier: 3.534A pdb=" N ILE S 124 " --> pdb=" O ARG S 120 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLN S 125 " --> pdb=" O ALA S 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 120 through 125' Processing helix chain 'S' and resid 139 through 147 removed outlier: 4.742A pdb=" N PHE S 145 " --> pdb=" O ALA S 141 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS S 146 " --> pdb=" O VAL S 142 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP S 147 " --> pdb=" O LYS S 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 161 through 166 Proline residue: S 165 - end of helix No H-bonds generated for 'chain 'S' and resid 161 through 166' Processing helix chain 'T' and resid 11 through 16 removed outlier: 3.521A pdb=" N PHE T 15 " --> pdb=" O THR T 11 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER T 16 " --> pdb=" O ARG T 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 11 through 16' Processing helix chain 'T' and resid 26 through 32 removed outlier: 4.591A pdb=" N TYR T 30 " --> pdb=" O PRO T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 59 removed outlier: 3.684A pdb=" N HIS T 58 " --> pdb=" O HIS T 54 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLY T 59 " --> pdb=" O LYS T 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 54 through 59' Processing helix chain 'T' and resid 92 through 97 removed outlier: 4.416A pdb=" N ILE T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LYS T 97 " --> pdb=" O ILE T 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 92 through 97' Processing helix chain 'T' and resid 99 through 120 removed outlier: 4.537A pdb=" N ASP T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE T 105 " --> pdb=" O SER T 101 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS T 120 " --> pdb=" O LYS T 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 32 removed outlier: 3.959A pdb=" N VAL U 29 " --> pdb=" O CYS U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 47 removed outlier: 3.660A pdb=" N PHE U 39 " --> pdb=" O ASP U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 60 removed outlier: 4.840A pdb=" N GLY U 59 " --> pdb=" O ASN U 55 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL U 60 " --> pdb=" O LEU U 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 55 through 60' Processing helix chain 'U' and resid 79 through 95 removed outlier: 3.961A pdb=" N LEU U 83 " --> pdb=" O SER U 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 69 through 74 removed outlier: 5.438A pdb=" N LYS V 74 " --> pdb=" O PRO V 70 " (cutoff:3.500A) Processing helix chain 'V' and resid 122 through 130 removed outlier: 3.505A pdb=" N LEU V 128 " --> pdb=" O GLU V 124 " (cutoff:3.500A) Proline residue: V 130 - end of helix Processing helix chain 'V' and resid 131 through 137 removed outlier: 5.179A pdb=" N GLY V 137 " --> pdb=" O ALA V 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 43 Processing helix chain 'W' and resid 45 through 50 removed outlier: 3.563A pdb=" N ILE W 49 " --> pdb=" O ASN W 45 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASN W 50 " --> pdb=" O PRO W 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 45 through 50' Processing helix chain 'W' and resid 52 through 60 removed outlier: 3.765A pdb=" N ARG W 56 " --> pdb=" O THR W 52 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 96 removed outlier: 3.553A pdb=" N ILE W 90 " --> pdb=" O SER W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 121 Processing helix chain 'X' and resid 72 through 78 removed outlier: 3.937A pdb=" N ILE X 77 " --> pdb=" O HIS X 73 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LYS X 78 " --> pdb=" O TYR X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 93 Processing helix chain 'X' and resid 105 through 117 Processing helix chain 'X' and resid 145 through 154 removed outlier: 3.595A pdb=" N VAL X 149 " --> pdb=" O ASP X 145 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 21 Processing helix chain 'Y' and resid 22 through 31 removed outlier: 4.041A pdb=" N LYS Y 28 " --> pdb=" O HIS Y 24 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER Y 31 " --> pdb=" O ARG Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 100 through 105 removed outlier: 4.086A pdb=" N VAL Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL Y 105 " --> pdb=" O PRO Y 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 100 through 105' Processing helix chain 'Y' and resid 112 through 134 Processing helix chain 'Z' and resid 58 through 67 removed outlier: 4.274A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 4.791A pdb=" N MET Z 81 " --> pdb=" O TYR Z 77 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 97 removed outlier: 4.692A pdb=" N ASN Z 97 " --> pdb=" O LYS Z 93 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 125 Processing helix chain 'Z' and resid 127 through 133 removed outlier: 3.859A pdb=" N PHE Z 131 " --> pdb=" O ASN Z 127 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN Z 132 " --> pdb=" O LYS Z 128 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS Z 133 " --> pdb=" O TRP Z 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 127 through 133' Processing helix chain 'a' and resid 2 through 7 removed outlier: 3.823A pdb=" N ARG a 6 " --> pdb=" O PRO a 2 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS a 7 " --> pdb=" O SER a 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 2 through 7' Processing helix chain 'a' and resid 41 through 49 Processing helix chain 'a' and resid 64 through 69 removed outlier: 3.940A pdb=" N SER a 68 " --> pdb=" O LYS a 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 83 removed outlier: 5.044A pdb=" N TRP a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR a 80 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N SER a 83 " --> pdb=" O TRP a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 93 Processing helix chain 'a' and resid 102 through 107 removed outlier: 3.938A pdb=" N SER a 106 " --> pdb=" O ASP a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 141 Processing helix chain 'b' and resid 11 through 20 removed outlier: 3.566A pdb=" N ARG b 18 " --> pdb=" O ARG b 14 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASN b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 55 removed outlier: 3.748A pdb=" N ASN b 50 " --> pdb=" O ALA b 46 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LYS b 51 " --> pdb=" O LYS b 47 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LYS b 52 " --> pdb=" O LYS b 48 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY b 53 " --> pdb=" O HIS b 49 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU b 54 " --> pdb=" O ASN b 50 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LYS b 55 " --> pdb=" O LYS b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 56 through 76 Processing helix chain 'b' and resid 90 through 102 removed outlier: 3.641A pdb=" N HIS b 94 " --> pdb=" O SER b 90 " (cutoff:3.500A) Proline residue: b 102 - end of helix Processing helix chain 'b' and resid 105 through 117 removed outlier: 3.618A pdb=" N ARG b 109 " --> pdb=" O GLY b 105 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 24 Processing helix chain 'c' and resid 30 through 41 removed outlier: 3.628A pdb=" N LYS c 36 " --> pdb=" O LYS c 32 " (cutoff:3.500A) Processing helix chain 'c' and resid 53 through 68 Processing helix chain 'c' and resid 77 through 86 Processing helix chain 'd' and resid 28 through 34 removed outlier: 3.897A pdb=" N ARG d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 57 removed outlier: 3.671A pdb=" N ARG d 44 " --> pdb=" O LYS d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 65 through 74 Processing helix chain 'e' and resid 24 through 29 removed outlier: 5.175A pdb=" N VAL e 29 " --> pdb=" O SER e 25 " (cutoff:3.500A) Processing helix chain 'e' and resid 43 through 48 removed outlier: 3.612A pdb=" N ARG e 47 " --> pdb=" O ASN e 43 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG e 48 " --> pdb=" O ARG e 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 43 through 48' Processing helix chain 'e' and resid 81 through 92 removed outlier: 3.517A pdb=" N LEU e 85 " --> pdb=" O ASN e 81 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU e 86 " --> pdb=" O VAL e 82 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL e 87 " --> pdb=" O LYS e 83 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU e 88 " --> pdb=" O GLU e 84 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU e 89 " --> pdb=" O LEU e 85 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N MET e 90 " --> pdb=" O GLU e 86 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N CYS e 91 " --> pdb=" O VAL e 87 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 119 removed outlier: 3.621A pdb=" N LYS e 109 " --> pdb=" O SER e 105 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA e 110 " --> pdb=" O LYS e 106 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 40 removed outlier: 4.167A pdb=" N GLU f 40 " --> pdb=" O ARG f 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 68 removed outlier: 3.736A pdb=" N LEU g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N MET g 65 " --> pdb=" O PRO g 61 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ARG g 66 " --> pdb=" O LYS g 62 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER g 68 " --> pdb=" O LEU g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 115 Processing helix chain 'h' and resid 5 through 13 removed outlier: 3.874A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG h 10 " --> pdb=" O ALA h 6 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY h 11 " --> pdb=" O ARG h 7 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LYS h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 5 through 13' Processing helix chain 'h' and resid 14 through 38 Processing helix chain 'h' and resid 40 through 74 removed outlier: 4.369A pdb=" N ARG h 48 " --> pdb=" O LEU h 44 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL h 49 " --> pdb=" O SER h 45 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN h 68 " --> pdb=" O THR h 64 " (cutoff:3.500A) Processing helix chain 'h' and resid 80 through 85 Proline residue: h 85 - end of helix Processing helix chain 'h' and resid 88 through 95 removed outlier: 6.265A pdb=" N LEU h 95 " --> pdb=" O MET h 91 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 102 Processing helix chain 'h' and resid 104 through 114 Processing helix chain 'i' and resid 25 through 30 removed outlier: 4.220A pdb=" N ARG i 29 " --> pdb=" O ARG i 25 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG i 30 " --> pdb=" O HIS i 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 25 through 30' Processing helix chain 'i' and resid 34 through 48 Processing helix chain 'i' and resid 51 through 64 Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 103 Processing helix chain 'j' and resid 4 through 11 removed outlier: 3.851A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS j 10 " --> pdb=" O SER j 6 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG j 11 " --> pdb=" O SER j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.573A pdb=" N ASN j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR j 58 " --> pdb=" O LYS j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 77 removed outlier: 4.284A pdb=" N ILE j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 18 removed outlier: 5.556A pdb=" N LYS k 18 " --> pdb=" O THR k 14 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 60 Processing helix chain 'l' and resid 6 through 21 removed outlier: 4.034A pdb=" N ARG l 21 " --> pdb=" O GLN l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.196A pdb=" N TRP l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS l 30 " --> pdb=" O TRP l 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 24 through 30' Processing helix chain 'm' and resid 53 through 65 Processing helix chain 'n' and resid 2 through 25 removed outlier: 3.567A pdb=" N ARG n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER n 24 " --> pdb=" O MET n 20 " (cutoff:3.500A) Processing helix chain 'o' and resid 35 through 46 Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.602A pdb=" N LYS p 28 " --> pdb=" O LYS p 24 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE p 29 " --> pdb=" O MET p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 Processing helix chain 'p' and resid 9 through 14 removed outlier: 3.613A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Processing helix chain 'r' and resid 2 through 11 Processing helix chain 'r' and resid 85 through 98 Processing helix chain 'r' and resid 103 through 123 removed outlier: 4.397A pdb=" N ARG r 107 " --> pdb=" O HIS r 103 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N MET r 108 " --> pdb=" O PRO r 104 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALA r 109 " --> pdb=" O ASP r 105 " (cutoff:3.500A) Proline residue: r 123 - end of helix Processing helix chain 's' and resid 5 through 25 removed outlier: 3.608A pdb=" N TRP s 9 " --> pdb=" O ASP s 5 " (cutoff:3.500A) Proline residue: s 25 - end of helix Processing helix chain 's' and resid 36 through 48 Processing helix chain 's' and resid 57 through 72 removed outlier: 3.697A pdb=" N GLU s 70 " --> pdb=" O ARG s 66 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN s 71 " --> pdb=" O GLY s 67 " (cutoff:3.500A) Processing helix chain 's' and resid 77 through 82 removed outlier: 4.568A pdb=" N HIS s 81 " --> pdb=" O LYS s 77 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE s 82 " --> pdb=" O LEU s 78 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 77 through 82' Processing helix chain 's' and resid 94 through 106 removed outlier: 4.019A pdb=" N ILE s 98 " --> pdb=" O ASP s 94 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS s 106 " --> pdb=" O LEU s 102 " (cutoff:3.500A) Processing helix chain 's' and resid 135 through 142 removed outlier: 4.855A pdb=" N LEU s 141 " --> pdb=" O PHE s 137 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY s 142 " --> pdb=" O PHE s 138 " (cutoff:3.500A) Processing helix chain 's' and resid 168 through 179 removed outlier: 3.523A pdb=" N ALA s 172 " --> pdb=" O GLY s 168 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU s 174 " --> pdb=" O SER s 170 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU s 175 " --> pdb=" O GLU s 171 " (cutoff:3.500A) Processing helix chain 't' and resid 30 through 36 Proline residue: t 34 - end of helix No H-bonds generated for 'chain 't' and resid 30 through 36' Processing helix chain 't' and resid 38 through 51 Processing helix chain 't' and resid 76 through 86 removed outlier: 4.511A pdb=" N LYS t 86 " --> pdb=" O ILE t 82 " (cutoff:3.500A) Processing helix chain 't' and resid 105 through 120 Processing helix chain 't' and resid 124 through 140 removed outlier: 3.908A pdb=" N THR t 128 " --> pdb=" O GLU t 124 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER t 138 " --> pdb=" O GLY t 134 " (cutoff:3.500A) Processing helix chain 't' and resid 146 through 157 removed outlier: 4.949A pdb=" N ASN t 156 " --> pdb=" O ILE t 152 " (cutoff:3.500A) Processing helix chain 'AA' and resid 11 through 22 removed outlier: 3.754A pdb=" N LEUAA 16 " --> pdb=" O GLUAA 12 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYSAA 17 " --> pdb=" O GLUAA 13 " (cutoff:3.500A) Processing helix chain 'AA' and resid 31 through 39 removed outlier: 3.644A pdb=" N GLUAA 35 " --> pdb=" O ASPAA 31 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLNAA 36 " --> pdb=" O PHEAA 32 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N TYRAA 37 " --> pdb=" O GLNAA 33 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILEAA 38 " --> pdb=" O METAA 34 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N TYRAA 39 " --> pdb=" O GLUAA 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'AA' and resid 31 through 39' Processing helix chain 'AA' and resid 50 through 69 removed outlier: 3.503A pdb=" N ILEAA 68 " --> pdb=" O ALAAA 64 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLUAA 69 " --> pdb=" O ILEAA 65 " (cutoff:3.500A) Processing helix chain 'AA' and resid 80 through 95 removed outlier: 3.728A pdb=" N GLNAA 84 " --> pdb=" O ARGAA 80 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARGAA 85 " --> pdb=" O ASNAA 81 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALAAA 86 " --> pdb=" O THRAA 82 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEUAA 88 " --> pdb=" O GLNAA 84 " (cutoff:3.500A) Processing helix chain 'AA' and resid 126 through 131 Processing helix chain 'AA' and resid 132 through 141 removed outlier: 3.744A pdb=" N TYRAA 139 " --> pdb=" O THRAA 135 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASNAA 141 " --> pdb=" O ALAAA 137 " (cutoff:3.500A) Processing helix chain 'AA' and resid 167 through 187 removed outlier: 3.649A pdb=" N GLYAA 172 " --> pdb=" O ALAAA 168 " (cutoff:3.500A) Processing helix chain 'AA' and resid 198 through 204 removed outlier: 4.383A pdb=" N TYRAA 202 " --> pdb=" O METAA 198 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHEAA 203 " --> pdb=" O PROAA 199 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYRAA 204 " --> pdb=" O ASPAA 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'AA' and resid 198 through 204' Processing helix chain 'AA' and resid 206 through 218 removed outlier: 3.517A pdb=" N GLUAA 211 " --> pdb=" O PROAA 207 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALAAA 218 " --> pdb=" O GLUAA 214 " (cutoff:3.500A) Processing helix chain 'AA' and resid 70 through 75 removed outlier: 5.075A pdb=" N SERAA 75 " --> pdb=" O ALAAA 72 " (cutoff:3.500A) Processing helix chain 'BB' and resid 23 through 29 removed outlier: 4.217A pdb=" N LYSBB 27 " --> pdb=" O ASPBB 23 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYSBB 28 " --> pdb=" O PROBB 24 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASPBB 29 " --> pdb=" O PHEBB 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'BB' and resid 23 through 29' Processing helix chain 'BB' and resid 57 through 65 removed outlier: 4.331A pdb=" N GLYBB 64 " --> pdb=" O ASPBB 60 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARGBB 65 " --> pdb=" O GLYBB 61 " (cutoff:3.500A) Processing helix chain 'BB' and resid 70 through 75 Processing helix chain 'BB' and resid 106 through 115 removed outlier: 5.145A pdb=" N LYSBB 115 " --> pdb=" O CYSBB 111 " (cutoff:3.500A) Processing helix chain 'BB' and resid 157 through 179 removed outlier: 3.918A pdb=" N THRBB 178 " --> pdb=" O ARGBB 174 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASNBB 179 " --> pdb=" O GLUBB 175 " (cutoff:3.500A) Processing helix chain 'BB' and resid 180 through 191 Proline residue: BB 190 - end of helix Processing helix chain 'BB' and resid 192 through 203 removed outlier: 3.520A pdb=" N ASPBB 196 " --> pdb=" O SERBB 192 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLNBB 202 " --> pdb=" O GLUBB 198 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SERBB 203 " --> pdb=" O LYSBB 199 " (cutoff:3.500A) Processing helix chain 'BB' and resid 224 through 233 removed outlier: 3.705A pdb=" N GLYBB 233 " --> pdb=" O METBB 229 " (cutoff:3.500A) Processing helix chain 'CC' and resid 64 through 73 removed outlier: 3.536A pdb=" N LEUCC 69 " --> pdb=" O LYSCC 65 " (cutoff:3.500A) Processing helix chain 'CC' and resid 77 through 85 removed outlier: 3.811A pdb=" N ILECC 81 " --> pdb=" O SERCC 77 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHECC 84 " --> pdb=" O GLUCC 80 " (cutoff:3.500A) Processing helix chain 'CC' and resid 90 through 98 removed outlier: 4.670A pdb=" N ILECC 94 " --> pdb=" O GLUCC 90 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASPCC 95 " --> pdb=" O SERCC 91 " (cutoff:3.500A) Processing helix chain 'CC' and resid 146 through 162 Processing helix chain 'CC' and resid 207 through 218 removed outlier: 3.512A pdb=" N GLYCC 218 " --> pdb=" O LEUCC 214 " (cutoff:3.500A) Processing helix chain 'CC' and resid 232 through 248 removed outlier: 3.661A pdb=" N THRCC 247 " --> pdb=" O ALACC 243 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TYRCC 248 " --> pdb=" O ILECC 244 " (cutoff:3.500A) Processing helix chain 'CC' and resid 252 through 257 removed outlier: 3.731A pdb=" N TRPCC 256 " --> pdb=" O THRCC 252 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYSCC 257 " --> pdb=" O PROCC 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'CC' and resid 252 through 257' Processing helix chain 'CC' and resid 264 through 270 removed outlier: 3.611A pdb=" N THRCC 270 " --> pdb=" O TYRCC 266 " (cutoff:3.500A) Processing helix chain 'CC' and resid 271 through 277 removed outlier: 3.995A pdb=" N LYSCC 275 " --> pdb=" O ASPCC 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HISCC 277 " --> pdb=" O LEUCC 273 " (cutoff:3.500A) Processing helix chain 'DD' and resid 6 through 29 removed outlier: 3.897A pdb=" N VALDD 12 " --> pdb=" O LYSDD 8 " (cutoff:3.500A) Processing helix chain 'DD' and resid 54 through 60 Processing helix chain 'DD' and resid 63 through 78 removed outlier: 3.550A pdb=" N ARGDD 67 " --> pdb=" O GLYDD 63 " (cutoff:3.500A) Processing helix chain 'DD' and resid 93 through 98 removed outlier: 4.272A pdb=" N CYSDD 97 " --> pdb=" O THRDD 93 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ALADD 98 " --> pdb=" O ARGDD 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'DD' and resid 93 through 98' Processing helix chain 'DD' and resid 99 through 112 Processing helix chain 'DD' and resid 114 through 130 Processing helix chain 'DD' and resid 161 through 167 removed outlier: 4.991A pdb=" N ASNDD 165 " --> pdb=" O GLYDD 161 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYRDD 166 " --> pdb=" O ASPDD 162 " (cutoff:3.500A) Processing helix chain 'EE' and resid 43 through 49 Processing helix chain 'EE' and resid 57 through 68 removed outlier: 3.829A pdb=" N ARGEE 68 " --> pdb=" O ILEEE 64 " (cutoff:3.500A) Processing helix chain 'EE' and resid 115 through 122 removed outlier: 4.682A pdb=" N TYREE 121 " --> pdb=" O GLUEE 117 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYSEE 122 " --> pdb=" O GLUEE 118 " (cutoff:3.500A) Processing helix chain 'EE' and resid 221 through 226 removed outlier: 4.245A pdb=" N ILEEE 225 " --> pdb=" O ARGEE 221 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N PHEEE 226 " --> pdb=" O LEUEE 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'EE' and resid 221 through 226' Processing helix chain 'EE' and resid 247 through 263 Processing helix chain 'FF' and resid 32 through 37 removed outlier: 4.848A pdb=" N ASPFF 37 " --> pdb=" O ILEFF 33 " (cutoff:3.500A) Processing helix chain 'FF' and resid 61 through 67 removed outlier: 4.147A pdb=" N GLNFF 65 " --> pdb=" O PHEFF 61 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYSFF 66 " --> pdb=" O ARGFF 62 " (cutoff:3.500A) Proline residue: FF 67 - end of helix No H-bonds generated for 'chain 'FF' and resid 61 through 67' Processing helix chain 'FF' and resid 68 through 78 removed outlier: 3.561A pdb=" N METFF 77 " --> pdb=" O THRFF 73 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N METFF 78 " --> pdb=" O ASNFF 74 " (cutoff:3.500A) Processing helix chain 'FF' and resid 85 through 104 Processing helix chain 'FF' and resid 107 through 120 Processing helix chain 'FF' and resid 142 through 164 removed outlier: 5.866A pdb=" N ARGFF 164 " --> pdb=" O GLUFF 160 " (cutoff:3.500A) Processing helix chain 'FF' and resid 168 through 183 Processing helix chain 'FF' and resid 187 through 204 removed outlier: 3.564A pdb=" N ARGFF 204 " --> pdb=" O ALAFF 200 " (cutoff:3.500A) Processing helix chain 'GG' and resid 20 through 29 removed outlier: 4.803A pdb=" N THRGG 26 " --> pdb=" O ARGGG 22 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHEGG 27 " --> pdb=" O LYSGG 23 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLUGG 29 " --> pdb=" O ARGGG 25 " (cutoff:3.500A) Processing helix chain 'GG' and resid 38 through 43 removed outlier: 4.043A pdb=" N GLYGG 42 " --> pdb=" O ALAGG 38 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLUGG 43 " --> pdb=" O ASPGG 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'GG' and resid 38 through 43' Processing helix chain 'GG' and resid 137 through 146 Processing helix chain 'GG' and resid 152 through 157 removed outlier: 4.853A pdb=" N TYRGG 156 " --> pdb=" O ASPGG 152 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VALGG 157 " --> pdb=" O VALGG 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'GG' and resid 152 through 157' Processing helix chain 'GG' and resid 181 through 237 removed outlier: 3.528A pdb=" N LYSGG 195 " --> pdb=" O ARGGG 191 " (cutoff:3.500A) Processing helix chain 'GG' and resid 121 through 126 Processing helix chain 'HH' and resid 17 through 34 Processing helix chain 'HH' and resid 36 through 44 removed outlier: 4.231A pdb=" N GLUHH 42 " --> pdb=" O ALAHH 38 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEUHH 43 " --> pdb=" O GLNHH 39 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASNHH 44 " --> pdb=" O LEUHH 40 " (cutoff:3.500A) Processing helix chain 'HH' and resid 65 through 76 removed outlier: 4.584A pdb=" N LYSHH 70 " --> pdb=" O VALHH 66 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N SERHH 71 " --> pdb=" O PROHH 67 " (cutoff:3.500A) Processing helix chain 'HH' and resid 77 through 88 removed outlier: 3.856A pdb=" N SERHH 88 " --> pdb=" O GLUHH 84 " (cutoff:3.500A) Processing helix chain 'HH' and resid 117 through 122 removed outlier: 3.732A pdb=" N THRHH 121 " --> pdb=" O PROHH 117 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEUHH 122 " --> pdb=" O ARGHH 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'HH' and resid 117 through 122' Processing helix chain 'HH' and resid 123 through 135 removed outlier: 3.560A pdb=" N LEUHH 130 " --> pdb=" O HISHH 126 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VALHH 134 " --> pdb=" O LEUHH 130 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHEHH 135 " --> pdb=" O GLUHH 131 " (cutoff:3.500A) Processing helix chain 'HH' and resid 159 through 164 removed outlier: 4.242A pdb=" N GLNHH 163 " --> pdb=" O ASPHH 159 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASNHH 164 " --> pdb=" O LYSHH 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'HH' and resid 159 through 164' Processing helix chain 'HH' and resid 165 through 171 removed outlier: 5.338A pdb=" N LYSHH 169 " --> pdb=" O ASNHH 165 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VALHH 170 " --> pdb=" O VALHH 166 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLUHH 171 " --> pdb=" O GLUHH 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'HH' and resid 165 through 171' Processing helix chain 'HH' and resid 172 through 181 Processing helix chain 'II' and resid 25 through 30 removed outlier: 4.146A pdb=" N LEUII 29 " --> pdb=" O ARGII 25 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLYII 30 " --> pdb=" O LYSII 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'II' and resid 25 through 30' Processing helix chain 'II' and resid 87 through 94 removed outlier: 3.924A pdb=" N VALII 91 " --> pdb=" O ASNII 87 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYSII 94 " --> pdb=" O LEUII 90 " (cutoff:3.500A) Processing helix chain 'II' and resid 106 through 117 Processing helix chain 'II' and resid 132 through 140 removed outlier: 4.661A pdb=" N LYSII 140 " --> pdb=" O ILEII 136 " (cutoff:3.500A) Processing helix chain 'II' and resid 142 through 157 removed outlier: 3.780A pdb=" N LYSII 147 " --> pdb=" O LYSII 143 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASNII 155 " --> pdb=" O GLUII 151 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALAII 156 " --> pdb=" O ARGII 152 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYSII 157 " --> pdb=" O LYSII 153 " (cutoff:3.500A) Processing helix chain 'II' and resid 159 through 169 Processing helix chain 'II' and resid 192 through 207 Processing helix chain 'JJ' and resid 21 through 36 Processing helix chain 'JJ' and resid 39 through 64 removed outlier: 3.544A pdb=" N VALJJ 43 " --> pdb=" O ASNJJ 39 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILEJJ 53 " --> pdb=" O THRJJ 49 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEUJJ 63 " --> pdb=" O GLUJJ 59 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASPJJ 64 " --> pdb=" O LEUJJ 60 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 67 through 85 Processing helix chain 'JJ' and resid 93 through 100 removed outlier: 3.929A pdb=" N ILEJJ 97 " --> pdb=" O LYSJJ 93 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEUJJ 98 " --> pdb=" O LEUJJ 94 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLYJJ 99 " --> pdb=" O ASPJJ 95 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEUJJ 100 " --> pdb=" O TYRJJ 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'JJ' and resid 93 through 100' Processing helix chain 'JJ' and resid 101 through 109 removed outlier: 4.043A pdb=" N PHEJJ 105 " --> pdb=" O LYSJJ 101 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARGJJ 109 " --> pdb=" O PHEJJ 105 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 110 through 118 removed outlier: 3.512A pdb=" N PHEJJ 115 " --> pdb=" O GLNJJ 111 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLYJJ 118 " --> pdb=" O VALJJ 114 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 122 through 133 removed outlier: 3.528A pdb=" N ARGJJ 127 " --> pdb=" O ILEJJ 123 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VALJJ 128 " --> pdb=" O HISJJ 124 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 150 through 155 removed outlier: 5.109A pdb=" N LYSJJ 155 " --> pdb=" O LEUJJ 151 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 171 through 186 Processing helix chain 'KK' and resid 4 through 19 removed outlier: 3.708A pdb=" N GLYKK 19 " --> pdb=" O LEUKK 15 " (cutoff:3.500A) Processing helix chain 'KK' and resid 41 through 56 removed outlier: 3.559A pdb=" N ARGKK 55 " --> pdb=" O SERKK 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLYKK 56 " --> pdb=" O LEUKK 52 " (cutoff:3.500A) Processing helix chain 'KK' and resid 72 through 84 Processing helix chain 'KK' and resid 91 through 96 removed outlier: 5.003A pdb=" N ARGKK 96 " --> pdb=" O ALAKK 92 " (cutoff:3.500A) Processing helix chain 'LL' and resid 47 through 53 removed outlier: 3.588A pdb=" N ILELL 51 " --> pdb=" O PROLL 47 " (cutoff:3.500A) Processing helix chain 'MM' and resid 14 through 29 removed outlier: 3.556A pdb=" N GLUMM 20 " --> pdb=" O THRMM 16 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEUMM 26 " --> pdb=" O LEUMM 22 " (cutoff:3.500A) Processing helix chain 'MM' and resid 34 through 45 Processing helix chain 'MM' and resid 59 through 73 removed outlier: 4.000A pdb=" N LYSMM 63 " --> pdb=" O PROMM 59 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VALMM 65 " --> pdb=" O TYRMM 61 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N HISMM 72 " --> pdb=" O LEUMM 68 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLNMM 73 " --> pdb=" O CYSMM 69 " (cutoff:3.500A) Processing helix chain 'MM' and resid 81 through 90 Processing helix chain 'MM' and resid 118 through 130 removed outlier: 3.604A pdb=" N VALMM 123 " --> pdb=" O GLNMM 119 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILEMM 124 " --> pdb=" O ALAMM 120 " (cutoff:3.500A) Processing helix chain 'NN' and resid 29 through 44 Processing helix chain 'NN' and resid 46 through 57 Processing helix chain 'NN' and resid 62 through 67 Processing helix chain 'NN' and resid 70 through 79 Processing helix chain 'NN' and resid 85 through 106 removed outlier: 3.752A pdb=" N ARGNN 104 " --> pdb=" O LYSNN 100 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARGNN 106 " --> pdb=" O LEUNN 102 " (cutoff:3.500A) Processing helix chain 'NN' and resid 108 through 133 removed outlier: 3.800A pdb=" N LYSNN 112 " --> pdb=" O ASPNN 108 " (cutoff:3.500A) Processing helix chain 'NN' and resid 145 through 150 removed outlier: 4.538A pdb=" N LEUNN 149 " --> pdb=" O THRNN 145 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VALNN 150 " --> pdb=" O ALANN 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'NN' and resid 145 through 150' Processing helix chain 'OO' and resid 57 through 63 removed outlier: 3.732A pdb=" N LYSOO 61 " --> pdb=" O THROO 57 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYSOO 63 " --> pdb=" O GLYOO 59 " (cutoff:3.500A) Processing helix chain 'OO' and resid 64 through 69 removed outlier: 3.726A pdb=" N GLUOO 68 " --> pdb=" O ALAOO 64 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N SEROO 69 " --> pdb=" O ASPOO 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'OO' and resid 64 through 69' Processing helix chain 'OO' and resid 70 through 89 removed outlier: 3.690A pdb=" N LEUOO 88 " --> pdb=" O ARGOO 84 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLYOO 89 " --> pdb=" O CYSOO 85 " (cutoff:3.500A) Processing helix chain 'OO' and resid 109 through 123 removed outlier: 4.995A pdb=" N GLNOO 113 " --> pdb=" O GLYOO 109 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SEROO 114 " --> pdb=" O PROOO 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLYOO 123 " --> pdb=" O LEUOO 119 " (cutoff:3.500A) Processing helix chain 'PP' and resid 21 through 28 removed outlier: 3.915A pdb=" N METPP 28 " --> pdb=" O GLNPP 24 " (cutoff:3.500A) Processing helix chain 'PP' and resid 29 through 38 removed outlier: 5.379A pdb=" N SERPP 38 " --> pdb=" O METPP 34 " (cutoff:3.500A) Processing helix chain 'PP' and resid 39 through 48 Processing helix chain 'PP' and resid 50 through 68 removed outlier: 3.611A pdb=" N LEUPP 56 " --> pdb=" O LYSPP 52 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEUPP 57 " --> pdb=" O GLNPP 53 " (cutoff:3.500A) Proline residue: PP 68 - end of helix Processing helix chain 'PP' and resid 86 through 91 removed outlier: 6.142A pdb=" N GLYPP 91 " --> pdb=" O PROPP 87 " (cutoff:3.500A) Processing helix chain 'PP' and resid 115 through 121 removed outlier: 4.228A pdb=" N PHEPP 119 " --> pdb=" O TYRPP 115 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SERPP 120 " --> pdb=" O LEUPP 116 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILEPP 121 " --> pdb=" O GLYPP 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'PP' and resid 115 through 121' Processing helix chain 'QQ' and resid 44 through 59 removed outlier: 4.156A pdb=" N GLNQQ 48 " --> pdb=" O PROQQ 44 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N TYRQQ 49 " --> pdb=" O ARGQQ 45 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LYSQQ 50 " --> pdb=" O THRQQ 46 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEUQQ 51 " --> pdb=" O LEUQQ 47 " (cutoff:3.500A) Proline residue: QQ 54 - end of helix Processing helix chain 'QQ' and resid 60 through 67 removed outlier: 4.567A pdb=" N GLYQQ 65 " --> pdb=" O GLUQQ 61 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VALQQ 66 " --> pdb=" O ARGQQ 62 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASPQQ 67 " --> pdb=" O PHEQQ 63 " (cutoff:3.500A) Processing helix chain 'QQ' and resid 77 through 99 removed outlier: 3.548A pdb=" N ILEQQ 81 " --> pdb=" O HISQQ 77 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SERQQ 89 " --> pdb=" O ARGQQ 85 " (cutoff:3.500A) Processing helix chain 'QQ' and resid 101 through 116 removed outlier: 3.530A pdb=" N TYRQQ 115 " --> pdb=" O ILEQQ 111 " (cutoff:3.500A) Processing helix chain 'RR' and resid 6 through 20 removed outlier: 3.522A pdb=" N ALARR 12 " --> pdb=" O THRRR 8 " (cutoff:3.500A) Processing helix chain 'RR' and resid 27 through 39 removed outlier: 3.669A pdb=" N ARGRR 33 " --> pdb=" O HISRR 29 " (cutoff:3.500A) Processing helix chain 'RR' and resid 43 through 64 removed outlier: 3.507A pdb=" N ARGRR 47 " --> pdb=" O SERRR 43 " (cutoff:3.500A) Processing helix chain 'RR' and resid 71 through 84 removed outlier: 3.572A pdb=" N TYRRR 84 " --> pdb=" O ARGRR 80 " (cutoff:3.500A) Processing helix chain 'RR' and resid 99 through 110 removed outlier: 4.077A pdb=" N ASPRR 110 " --> pdb=" O LEURR 106 " (cutoff:3.500A) Processing helix chain 'SS' and resid 26 through 33 removed outlier: 4.263A pdb=" N THRSS 31 " --> pdb=" O ALASS 27 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALASS 32 " --> pdb=" O PHESS 28 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILESS 33 " --> pdb=" O ALASS 29 " (cutoff:3.500A) Processing helix chain 'SS' and resid 37 through 49 removed outlier: 4.653A pdb=" N ASPSS 49 " --> pdb=" O LEUSS 45 " (cutoff:3.500A) Processing helix chain 'SS' and resid 60 through 74 removed outlier: 3.563A pdb=" N THRSS 69 " --> pdb=" O GLUSS 65 " (cutoff:3.500A) Proline residue: SS 74 - end of helix Processing helix chain 'SS' and resid 100 through 118 removed outlier: 3.902A pdb=" N ASPSS 104 " --> pdb=" O ALASS 100 " (cutoff:3.500A) Processing helix chain 'SS' and resid 119 through 128 removed outlier: 3.520A pdb=" N HISSS 125 " --> pdb=" O ARGSS 121 " (cutoff:3.500A) Processing helix chain 'SS' and resid 140 through 145 removed outlier: 4.445A pdb=" N ARGSS 144 " --> pdb=" O GLYSS 140 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THRSS 145 " --> pdb=" O ARGSS 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'SS' and resid 140 through 145' Processing helix chain 'TT' and resid 5 through 10 removed outlier: 5.124A pdb=" N ASNTT 10 " --> pdb=" O VALTT 6 " (cutoff:3.500A) Processing helix chain 'TT' and resid 11 through 26 removed outlier: 3.585A pdb=" N VALTT 15 " --> pdb=" O GLNTT 11 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARGTT 16 " --> pdb=" O GLNTT 12 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLYTT 26 " --> pdb=" O LEUTT 22 " (cutoff:3.500A) Processing helix chain 'TT' and resid 51 through 67 removed outlier: 3.662A pdb=" N THRTT 55 " --> pdb=" O ASNTT 51 " (cutoff:3.500A) Processing helix chain 'TT' and resid 71 through 80 removed outlier: 3.542A pdb=" N METTT 75 " --> pdb=" O GLYTT 71 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLYTT 80 " --> pdb=" O THRTT 76 " (cutoff:3.500A) Processing helix chain 'TT' and resid 96 through 111 removed outlier: 3.786A pdb=" N ALATT 100 " --> pdb=" O SERTT 96 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYSTT 111 " --> pdb=" O LEUTT 107 " (cutoff:3.500A) Processing helix chain 'TT' and resid 124 through 143 removed outlier: 3.618A pdb=" N GLYTT 136 " --> pdb=" O ASPTT 132 " (cutoff:3.500A) Processing helix chain 'UU' and resid 28 through 47 removed outlier: 3.812A pdb=" N LEUUU 32 " --> pdb=" O ASNUU 28 " (cutoff:3.500A) Processing helix chain 'UU' and resid 94 through 106 removed outlier: 3.594A pdb=" N VALUU 98 " --> pdb=" O PROUU 94 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILEUU 104 " --> pdb=" O GLNUU 100 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SERUU 105 " --> pdb=" O ILEUU 101 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ILEUU 106 " --> pdb=" O THRUU 102 " (cutoff:3.500A) Processing helix chain 'VV' and resid 56 through 63 removed outlier: 3.801A pdb=" N ARGVV 60 " --> pdb=" O CYSVV 56 " (cutoff:3.500A) Processing helix chain 'VV' and resid 64 through 77 Processing helix chain 'WW' and resid 5 through 21 removed outlier: 3.596A pdb=" N ARGWW 20 " --> pdb=" O ASNWW 16 " (cutoff:3.500A) Processing helix chain 'WW' and resid 31 through 45 Processing helix chain 'WW' and resid 82 through 94 removed outlier: 4.335A pdb=" N GLUWW 87 " --> pdb=" O LEUWW 83 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYSWW 88 " --> pdb=" O LYSWW 84 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEUWW 94 " --> pdb=" O GLNWW 90 " (cutoff:3.500A) Processing helix chain 'WW' and resid 112 through 120 Processing helix chain 'XX' and resid 9 through 24 removed outlier: 4.270A pdb=" N TRPXX 22 " --> pdb=" O ARGXX 18 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HISXX 23 " --> pdb=" O ASPXX 19 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASPXX 24 " --> pdb=" O GLNXX 20 " (cutoff:3.500A) Processing helix chain 'XX' and resid 25 through 32 Processing helix chain 'XX' and resid 33 through 40 Proline residue: XX 40 - end of helix Processing helix chain 'XX' and resid 89 through 95 removed outlier: 4.478A pdb=" N PHEXX 93 " --> pdb=" O GLYXX 89 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLUXX 95 " --> pdb=" O LEUXX 91 " (cutoff:3.500A) Processing helix chain 'XX' and resid 129 through 136 Processing helix chain 'YY' and resid 36 through 49 removed outlier: 3.709A pdb=" N LYSYY 46 " --> pdb=" O GLUYY 42 " (cutoff:3.500A) Processing helix chain 'YY' and resid 51 through 56 removed outlier: 4.063A pdb=" N ILEYY 55 " --> pdb=" O THRYY 51 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N PHEYY 56 " --> pdb=" O PROYY 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'YY' and resid 51 through 56' Processing helix chain 'YY' and resid 78 through 86 Processing helix chain 'YY' and resid 87 through 95 removed outlier: 4.199A pdb=" N HISYY 94 " --> pdb=" O ARGYY 90 " (cutoff:3.500A) Processing helix chain 'YY' and resid 103 through 118 removed outlier: 3.663A pdb=" N VALYY 117 " --> pdb=" O ARGYY 113 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ARGYY 118 " --> pdb=" O METYY 114 " (cutoff:3.500A) Processing helix chain 'YY' and resid 119 through 126 removed outlier: 4.788A pdb=" N ALAYY 123 " --> pdb=" O GLYYY 119 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASNYY 124 " --> pdb=" O THRYY 120 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLYYY 126 " --> pdb=" O LYSYY 122 " (cutoff:3.500A) Processing helix chain 'ZZ' and resid 51 through 65 Proline residue: ZZ 63 - end of helix Processing helix chain 'ZZ' and resid 69 through 78 Processing helix chain 'ZZ' and resid 80 through 95 removed outlier: 3.626A pdb=" N ARGZZ 85 " --> pdb=" O GLYZZ 81 " (cutoff:3.500A) Processing helix chain 'aa' and resid 47 through 57 removed outlier: 3.774A pdb=" N ARGaa 51 " --> pdb=" O ALAaa 47 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLUaa 55 " --> pdb=" O ARGaa 51 " (cutoff:3.500A) Processing helix chain 'aa' and resid 74 through 82 Processing helix chain 'aa' and resid 88 through 94 removed outlier: 4.358A pdb=" N LYSaa 93 " --> pdb=" O ARGaa 89 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASPaa 94 " --> pdb=" O GLUaa 90 " (cutoff:3.500A) Processing helix chain 'bb' and resid 11 through 19 removed outlier: 3.658A pdb=" N LYSbb 18 " --> pdb=" O GLUbb 14 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N HISbb 19 " --> pdb=" O GLUbb 15 " (cutoff:3.500A) Processing helix chain 'dd' and resid 2 through 9 removed outlier: 3.647A pdb=" N LEUdd 6 " --> pdb=" O GLYdd 2 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TRPdd 8 " --> pdb=" O GLNdd 4 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N SERdd 9 " --> pdb=" O GLNdd 5 " (cutoff:3.500A) Processing helix chain 'dd' and resid 15 through 20 removed outlier: 3.649A pdb=" N ARGdd 19 " --> pdb=" O GLYdd 15 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SERdd 20 " --> pdb=" O GLNdd 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'dd' and resid 15 through 20' Processing helix chain 'dd' and resid 39 through 47 Processing helix chain 'ee' and resid 83 through 89 removed outlier: 3.515A pdb=" N GLYee 87 " --> pdb=" O GLYee 83 " (cutoff:3.500A) Processing helix chain 'ee' and resid 103 through 115 Processing helix chain 'ff' and resid 100 through 107 removed outlier: 4.496A pdb=" N LYSff 104 " --> pdb=" O LEUff 100 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYRff 105 " --> pdb=" O ALAff 101 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYRff 106 " --> pdb=" O VALff 102 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LYSff 107 " --> pdb=" O LEUff 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'ff' and resid 100 through 107' Processing helix chain 'jj' and resid 19 through 32 removed outlier: 3.690A pdb=" N GLYjj 32 " --> pdb=" O ILEjj 28 " (cutoff:3.500A) Processing helix chain 'jj' and resid 35 through 50 removed outlier: 3.667A pdb=" N ILEjj 39 " --> pdb=" O ASPjj 35 " (cutoff:3.500A) Processing helix chain 'jj' and resid 54 through 62 removed outlier: 4.007A pdb=" N VALjj 59 " --> pdb=" O LYSjj 55 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEUjj 60 " --> pdb=" O TYRjj 56 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYSjj 62 " --> pdb=" O TRPjj 58 " (cutoff:3.500A) Processing helix chain 'jj' and resid 63 through 70 Processing helix chain 'jj' and resid 98 through 110 removed outlier: 3.757A pdb=" N GLNjj 108 " --> pdb=" O THRjj 104 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALAjj 109 " --> pdb=" O GLYjj 105 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASPjj 110 " --> pdb=" O THRjj 106 " (cutoff:3.500A) Processing helix chain 'jj' and resid 119 through 128 removed outlier: 3.671A pdb=" N PHEjj 123 " --> pdb=" O GLYjj 119 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLUjj 124 " --> pdb=" O VALjj 120 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SERjj 128 " --> pdb=" O GLUjj 124 " (cutoff:3.500A) Processing helix chain 'jj' and resid 131 through 144 removed outlier: 4.533A pdb=" N GLUjj 135 " --> pdb=" O GLYjj 131 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALAjj 137 " --> pdb=" O THRjj 133 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYRjj 141 " --> pdb=" O ALAjj 137 " (cutoff:3.500A) Processing helix chain 'jj' and resid 164 through 182 removed outlier: 3.507A pdb=" N TYRjj 177 " --> pdb=" O GLUjj 173 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYSjj 180 " --> pdb=" O THRjj 176 " (cutoff:3.500A) Processing helix chain 'jj' and resid 184 through 189 removed outlier: 5.151A pdb=" N ALAjj 189 " --> pdb=" O PROjj 185 " (cutoff:3.500A) Processing helix chain 'jj' and resid 227 through 235 removed outlier: 3.584A pdb=" N ILEjj 235 " --> pdb=" O ALAjj 231 " (cutoff:3.500A) Processing helix chain 'jj' and resid 316 through 321 removed outlier: 3.729A pdb=" N VALjj 320 " --> pdb=" O SERjj 316 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARGjj 321 " --> pdb=" O VALjj 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'jj' and resid 316 through 321' Processing helix chain 'jj' and resid 418 through 423 removed outlier: 3.815A pdb=" N ARGjj 423 " --> pdb=" O PROjj 419 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.589A pdb=" N ASP A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 44 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 134 through 137 removed outlier: 6.671A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 58 through 64 Processing sheet with id= 4, first strand: chain 'B' and resid 40 through 44 removed outlier: 4.881A pdb=" N HIS B 179 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU B 163 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN B 203 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 53 through 59 removed outlier: 6.703A pdb=" N ILE B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG B 343 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL B 344 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 222 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 348 " --> pdb=" O ASP B 218 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 98 through 102 removed outlier: 6.449A pdb=" N GLY B 91 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 76 through 80 No H-bonds generated for sheet with id= 7 Processing sheet with id= 8, first strand: chain 'B' and resid 88 through 93 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.987A pdb=" N GLU B 215 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 6 through 10 removed outlier: 5.381A pdb=" N LYS C 20 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 226 through 232 removed outlier: 3.902A pdb=" N THR C 228 " --> pdb=" O PRO C 207 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N PHE C 249 " --> pdb=" O GLY C 206 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 60 through 66 removed outlier: 3.641A pdb=" N VAL D 53 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 93 through 98 removed outlier: 5.977A pdb=" N ALA E 93 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 150 through 156 removed outlier: 4.296A pdb=" N THR E 151 " --> pdb=" O PHE E 167 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS E 163 " --> pdb=" O ILE E 155 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 157 through 160 removed outlier: 6.558A pdb=" N GLY F 157 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 209 through 212 removed outlier: 5.537A pdb=" N PHE F 117 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN F 118 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LYS F 87 " --> pdb=" O LEU F 124 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N TYR F 138 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TYR F 143 " --> pdb=" O ARG F 235 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 233 through 238 removed outlier: 3.599A pdb=" N LEU G 207 " --> pdb=" O PHE G 257 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 5 through 12 removed outlier: 3.677A pdb=" N GLN H 8 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS H 53 " --> pdb=" O ILE H 12 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG H 54 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.782A pdb=" N LYS H 28 " --> pdb=" O ASP H 17 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 25 " --> pdb=" O ARG H 36 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 102 through 106 removed outlier: 6.634A pdb=" N SER H 110 " --> pdb=" O MET H 128 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 132 through 136 removed outlier: 5.813A pdb=" N ASP H 142 " --> pdb=" O SER H 94 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER H 94 " --> pdb=" O ASP H 142 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 88 through 91 Processing sheet with id= 23, first strand: chain 'I' and resid 34 through 37 removed outlier: 6.256A pdb=" N PHE I 34 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ILE I 135 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET I 136 " --> pdb=" O MET I 52 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N CYS I 49 " --> pdb=" O SER I 168 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG I 162 " --> pdb=" O ASP I 55 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 95 through 98 Processing sheet with id= 25, first strand: chain 'I' and resid 189 through 193 removed outlier: 5.026A pdb=" N ARG I 189 " --> pdb=" O ILE I 200 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY I 196 " --> pdb=" O ASP I 193 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 48 through 52 removed outlier: 3.602A pdb=" N ALA J 69 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N CYS J 25 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N GLY J 127 " --> pdb=" O CYS J 25 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'J' and resid 92 through 96 removed outlier: 3.568A pdb=" N LEU J 175 " --> pdb=" O LEU J 94 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 11 through 16 removed outlier: 4.023A pdb=" N ARG M 11 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS M 23 " --> pdb=" O VAL M 15 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'M' and resid 28 through 31 removed outlier: 6.826A pdb=" N ARG M 35 " --> pdb=" O ILE M 31 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'N' and resid 35 through 39 removed outlier: 6.088A pdb=" N ALA N 35 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'N' and resid 117 through 123 removed outlier: 3.504A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU N 123 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR N 127 " --> pdb=" O GLU N 123 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 33, first strand: chain 'P' and resid 13 through 20 removed outlier: 7.556A pdb=" N LYS P 13 " --> pdb=" O GLU P 152 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU P 152 " --> pdb=" O LYS P 13 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE P 149 " --> pdb=" O GLU P 115 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'P' and resid 116 through 122 Processing sheet with id= 35, first strand: chain 'P' and resid 124 through 131 removed outlier: 3.687A pdb=" N SER P 141 " --> pdb=" O MET P 125 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG P 127 " --> pdb=" O TYR P 139 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG P 135 " --> pdb=" O ARG P 131 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Q' and resid 78 through 82 Processing sheet with id= 37, first strand: chain 'S' and resid 27 through 34 removed outlier: 6.731A pdb=" N VAL S 13 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'S' and resid 91 through 99 removed outlier: 3.742A pdb=" N MET S 93 " --> pdb=" O LEU S 82 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN S 77 " --> pdb=" O ILE S 132 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU S 130 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS S 128 " --> pdb=" O TRP S 81 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'S' and resid 9 through 13 removed outlier: 4.803A pdb=" N GLU S 9 " --> pdb=" O VAL S 67 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'T' and resid 39 through 42 removed outlier: 4.396A pdb=" N LYS T 60 " --> pdb=" O ILE T 42 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'T' and resid 73 through 79 Processing sheet with id= 42, first strand: chain 'U' and resid 61 through 65 removed outlier: 3.519A pdb=" N THR U 73 " --> pdb=" O SER U 62 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE U 70 " --> pdb=" O LEU U 23 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLU U 108 " --> pdb=" O LYS U 20 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU U 112 " --> pdb=" O ASP U 24 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'V' and resid 76 through 79 removed outlier: 6.773A pdb=" N MET V 62 " --> pdb=" O ILE V 40 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA V 24 " --> pdb=" O ILE V 39 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASN V 101 " --> pdb=" O VAL V 25 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 85 through 89 removed outlier: 5.734A pdb=" N LYS V 86 " --> pdb=" O PHE V 98 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N PHE V 98 " --> pdb=" O LYS V 86 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'W' and resid 3 through 7 removed outlier: 3.608A pdb=" N GLU W 4 " --> pdb=" O ILE W 13 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR W 11 " --> pdb=" O CYS W 6 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 18 through 22 Processing sheet with id= 47, first strand: chain 'X' and resid 94 through 100 removed outlier: 6.518A pdb=" N ASN X 94 " --> pdb=" O LEU X 140 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS X 134 " --> pdb=" O VAL X 100 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU X 133 " --> pdb=" O ARG X 129 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'Y' and resid 53 through 56 removed outlier: 4.799A pdb=" N ASP Y 53 " --> pdb=" O VAL Y 70 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Y' and resid 72 through 75 Processing sheet with id= 50, first strand: chain 'Y' and resid 86 through 89 removed outlier: 4.388A pdb=" N THR Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'Z' and resid 9 through 13 removed outlier: 5.508A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'Z' and resid 42 through 45 Processing sheet with id= 53, first strand: chain 'a' and resid 122 through 125 Processing sheet with id= 54, first strand: chain 'c' and resid 26 through 29 removed outlier: 6.589A pdb=" N LYS c 26 " --> pdb=" O ILE c 97 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU c 45 " --> pdb=" O ILE c 96 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY c 70 " --> pdb=" O LYS c 44 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'd' and resid 20 through 26 removed outlier: 3.518A pdb=" N VAL d 21 " --> pdb=" O ARG d 90 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG d 85 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER d 89 " --> pdb=" O LEU d 105 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP d 61 " --> pdb=" O LEU d 102 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'e' and resid 74 through 80 Processing sheet with id= 57, first strand: chain 'f' and resid 56 through 60 removed outlier: 5.657A pdb=" N THR f 57 " --> pdb=" O PRO f 64 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR f 59 " --> pdb=" O GLY f 62 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'f' and resid 8 through 12 removed outlier: 6.317A pdb=" N LYS f 8 " --> pdb=" O GLU f 31 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU f 27 " --> pdb=" O ALA f 12 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG f 85 " --> pdb=" O THR f 75 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS f 73 " --> pdb=" O LYS f 87 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS f 45 " --> pdb=" O VAL f 74 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ARG f 46 " --> pdb=" O MET f 104 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'f' and resid 6 through 12 removed outlier: 4.356A pdb=" N HIS f 99 " --> pdb=" O PHE f 11 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'g' and resid 19 through 24 removed outlier: 5.363A pdb=" N LYS g 19 " --> pdb=" O THR g 35 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 26 through 29 removed outlier: 8.004A pdb=" N ALA j 26 " --> pdb=" O GLY j 35 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'k' and resid 2 through 5 removed outlier: 3.705A pdb=" N ARG k 3 " --> pdb=" O LEU k 42 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL k 46 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN k 31 " --> pdb=" O ASN k 28 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN k 28 " --> pdb=" O ASN k 31 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER k 22 " --> pdb=" O ARG k 37 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS k 27 " --> pdb=" O LEU k 69 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'm' and resid 74 through 77 removed outlier: 5.692A pdb=" N LYS m 67 " --> pdb=" O LYS m 98 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ASN m 94 " --> pdb=" O ARG m 71 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'o' and resid 7 through 10 removed outlier: 5.564A pdb=" N VAL o 67 " --> pdb=" O TYR o 26 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'p' and resid 46 through 50 removed outlier: 8.617A pdb=" N LYS p 46 " --> pdb=" O GLY p 58 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY p 58 " --> pdb=" O LYS p 46 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'r' and resid 48 through 53 removed outlier: 4.807A pdb=" N THR r 48 " --> pdb=" O LYS r 65 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER r 76 " --> pdb=" O ARG r 66 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 's' and resid 51 through 55 removed outlier: 5.797A pdb=" N ASN s 85 " --> pdb=" O ALA s 32 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS s 26 " --> pdb=" O THR s 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN s 191 " --> pdb=" O ILE s 29 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER s 197 " --> pdb=" O ASP s 194 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 's' and resid 125 through 129 removed outlier: 4.224A pdb=" N GLN s 126 " --> pdb=" O ILE s 154 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE s 154 " --> pdb=" O GLN s 126 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE s 152 " --> pdb=" O THR s 128 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 't' and resid 11 through 16 Processing sheet with id= 70, first strand: chain 'AA' and resid 24 through 28 removed outlier: 5.139A pdb=" N HISAA 24 " --> pdb=" O ILEAA 49 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TYRAA 47 " --> pdb=" O GLYAA 26 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THRAA 28 " --> pdb=" O GLYAA 45 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLYAA 45 " --> pdb=" O THRAA 28 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'AA' and resid 121 through 125 removed outlier: 3.689A pdb=" N ILEAA 159 " --> pdb=" O THRAA 144 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALAAA 146 " --> pdb=" O ILEAA 159 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'BB' and resid 44 through 48 removed outlier: 4.113A pdb=" N GLYBB 45 " --> pdb=" O VALBB 33 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'BB' and resid 66 through 69 removed outlier: 3.699A pdb=" N GLYBB 102 " --> pdb=" O LYSBB 85 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N HISBB 101 " --> pdb=" O METBB 217 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N METBB 217 " --> pdb=" O HISBB 101 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ARGBB 213 " --> pdb=" O LEUBB 105 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEUBB 134 " --> pdb=" O LEUBB 218 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALABB 123 " --> pdb=" O CYSBB 139 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THRBB 119 " --> pdb=" O THRBB 143 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'CC' and resid 107 through 116 removed outlier: 3.634A pdb=" N LYSCC 108 " --> pdb=" O PHECC 127 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLYCC 119 " --> pdb=" O THRCC 116 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASPCC 132 " --> pdb=" O HISCC 136 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HISCC 136 " --> pdb=" O ASPCC 132 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'CC' and resid 183 through 187 removed outlier: 4.352A pdb=" N ALACC 198 " --> pdb=" O ASPCC 221 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASPCC 221 " --> pdb=" O ALACC 198 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'DD' and resid 35 through 42 removed outlier: 3.610A pdb=" N THRDD 42 " --> pdb=" O ARGDD 45 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARGDD 45 " --> pdb=" O THRDD 42 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLUDD 85 " --> pdb=" O THRDD 46 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILEDD 48 " --> pdb=" O GLUDD 85 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'DD' and resid 149 through 155 removed outlier: 3.607A pdb=" N ASPDD 154 " --> pdb=" O CYSDD 134 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SERDD 139 " --> pdb=" O GLYDD 183 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLYDD 180 " --> pdb=" O LEUDD 177 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'EE' and resid 88 through 92 removed outlier: 4.629A pdb=" N ASPEE 88 " --> pdb=" O LEUEE 101 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASNEE 98 " --> pdb=" O ILEEE 114 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HISEE 112 " --> pdb=" O ARGEE 100 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILEEE 102 " --> pdb=" O ALAEE 110 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'EE' and resid 123 through 126 removed outlier: 4.565A pdb=" N ASPEE 158 " --> pdb=" O VALEE 126 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASPEE 171 " --> pdb=" O GLNEE 161 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'EE' and resid 128 through 132 removed outlier: 3.788A pdb=" N LYSEE 128 " --> pdb=" O VALEE 140 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILEEE 136 " --> pdb=" O GLYEE 132 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'EE' and resid 197 through 200 removed outlier: 3.545A pdb=" N VALEE 207 " --> pdb=" O GLUEE 199 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'FF' and resid 123 through 127 Processing sheet with id= 83, first strand: chain 'GG' and resid 11 through 17 removed outlier: 5.950A pdb=" N ASNGG 110 " --> pdb=" O SERGG 53 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VALGG 49 " --> pdb=" O VALGG 114 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILEGG 52 " --> pdb=" O THRGG 34 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THRGG 34 " --> pdb=" O ILEGG 52 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'GG' and resid 73 through 76 Processing sheet with id= 85, first strand: chain 'GG' and resid 159 through 163 removed outlier: 4.157A pdb=" N ARGGG 170 " --> pdb=" O LEUGG 162 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'HH' and resid 46 through 53 removed outlier: 3.728A pdb=" N ALAHH 47 " --> pdb=" O PHEHH 63 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VALHH 53 " --> pdb=" O ARGHH 57 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARGHH 57 " --> pdb=" O VALHH 53 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HISHH 91 " --> pdb=" O LYSHH 58 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'HH' and resid 140 through 147 removed outlier: 4.105A pdb=" N SERHH 151 " --> pdb=" O LYSHH 147 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASPHH 184 " --> pdb=" O ARGHH 152 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'II' and resid 42 through 48 removed outlier: 6.330A pdb=" N ARGII 42 " --> pdb=" O LEUII 58 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASNII 52 " --> pdb=" O VALII 48 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'II' and resid 71 through 76 removed outlier: 3.728A pdb=" N PHEII 65 " --> pdb=" O ARGII 74 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASNII 64 " --> pdb=" O ALAII 185 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLYII 187 " --> pdb=" O ASNII 64 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLYII 68 " --> pdb=" O VALII 189 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASPII 186 " --> pdb=" O ALAII 176 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEUII 172 " --> pdb=" O LEUII 190 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYSII 100 " --> pdb=" O ILEII 175 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'KK' and resid 20 through 24 Processing sheet with id= 91, first strand: chain 'LL' and resid 71 through 76 removed outlier: 5.557A pdb=" N ARGLL 71 " --> pdb=" O GLULL 130 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THRLL 127 " --> pdb=" O LEULL 143 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARGLL 139 " --> pdb=" O CYSLL 131 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'LL' and resid 85 through 97 No H-bonds generated for sheet with id= 92 Processing sheet with id= 93, first strand: chain 'LL' and resid 124 through 127 removed outlier: 3.762A pdb=" N LYSLL 144 " --> pdb=" O THRLL 127 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'MM' and resid 75 through 80 removed outlier: 4.067A pdb=" N LEUMM 49 " --> pdb=" O VALMM 111 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'OO' and resid 40 through 46 removed outlier: 3.503A pdb=" N HISOO 43 " --> pdb=" O HISOO 32 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILEOO 95 " --> pdb=" O GLYOO 127 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'PP' and resid 75 through 78 Processing sheet with id= 97, first strand: chain 'QQ' and resid 8 through 15 removed outlier: 6.681A pdb=" N GLNQQ 8 " --> pdb=" O ARGQQ 27 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARGQQ 27 " --> pdb=" O GLNQQ 8 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALAQQ 21 " --> pdb=" O GLYQQ 14 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'RR' and resid 95 through 98 Processing sheet with id= 99, first strand: chain 'SS' and resid 11 through 14 removed outlier: 6.727A pdb=" N HISSS 11 " --> pdb=" O GLYSS 22 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'TT' and resid 113 through 116 removed outlier: 4.353A pdb=" N GLYTT 120 " --> pdb=" O ASPTT 116 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'UU' and resid 53 through 56 removed outlier: 5.048A pdb=" N LYSUU 86 " --> pdb=" O METUU 56 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N HISUU 18 " --> pdb=" O SERUU 93 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'UU' and resid 58 through 66 Processing sheet with id=103, first strand: chain 'VV' and resid 15 through 18 removed outlier: 4.412A pdb=" N ARGVV 15 " --> pdb=" O ILEVV 24 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARGVV 22 " --> pdb=" O CYSVV 17 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'VV' and resid 32 through 37 Processing sheet with id=105, first strand: chain 'WW' and resid 23 through 28 removed outlier: 5.326A pdb=" N ARGWW 23 " --> pdb=" O LEUWW 65 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASNWW 64 " --> pdb=" O GLUWW 49 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLUWW 49 " --> pdb=" O ASNWW 64 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'WW' and resid 71 through 74 Processing sheet with id=107, first strand: chain 'WW' and resid 78 through 81 removed outlier: 4.162A pdb=" N PHEWW 79 " --> pdb=" O ILEWW 125 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'XX' and resid 46 through 49 removed outlier: 6.491A pdb=" N LEUXX 101 " --> pdb=" O VALXX 123 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'XX' and resid 53 through 59 removed outlier: 3.513A pdb=" N GLUXX 53 " --> pdb=" O ARGXX 71 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ALAXX 65 " --> pdb=" O ALAXX 59 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LYSXX 68 " --> pdb=" O VALXX 85 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYSXX 79 " --> pdb=" O LEUXX 74 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'YY' and resid 5 through 10 Processing sheet with id=111, first strand: chain 'YY' and resid 59 through 63 removed outlier: 4.814A pdb=" N GLYYY 59 " --> pdb=" O PHEYY 72 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHEYY 72 " --> pdb=" O GLYYY 59 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LYSYY 68 " --> pdb=" O HISYY 63 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'YY' and resid 20 through 30 No H-bonds generated for sheet with id=112 Processing sheet with id=113, first strand: chain 'ZZ' and resid 97 through 100 removed outlier: 7.091A pdb=" N ILEZZ 108 " --> pdb=" O VALZZ 100 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'aa' and resid 36 through 43 removed outlier: 4.013A pdb=" N ARGaa 42 " --> pdb=" O LEUaa 67 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain 'bb' and resid 43 through 48 removed outlier: 7.059A pdb=" N TYRbb 31 " --> pdb=" O SERbb 48 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHEbb 32 " --> pdb=" O LYSbb 82 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARGbb 80 " --> pdb=" O ASPbb 34 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'cc' and resid 18 through 22 removed outlier: 7.097A pdb=" N ARGcc 31 " --> pdb=" O THRcc 15 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASPcc 54 " --> pdb=" O VALcc 14 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'cc' and resid 29 through 33 Processing sheet with id=118, first strand: chain 'ff' and resid 138 through 141 removed outlier: 3.501A pdb=" N HISff 139 " --> pdb=" O TYRff 148 " (cutoff:3.500A) Processing sheet with id=119, first strand: chain 'gg' and resid 3 through 7 removed outlier: 7.213A pdb=" N GLNgg 4 " --> pdb=" O THRgg 313 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLYgg 9 " --> pdb=" O VALgg 309 " (cutoff:3.500A) Processing sheet with id=120, first strand: chain 'gg' and resid 20 through 23 removed outlier: 4.570A pdb=" N GLNgg 20 " --> pdb=" O ALAgg 34 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASPgg 29 " --> pdb=" O LEUgg 45 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEUgg 45 " --> pdb=" O ASPgg 29 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILEgg 31 " --> pdb=" O TRPgg 43 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N METgg 42 " --> pdb=" O GLNgg 56 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYRgg 52 " --> pdb=" O THRgg 46 " (cutoff:3.500A) Processing sheet with id=121, first strand: chain 'gg' and resid 67 through 72 removed outlier: 3.704A pdb=" N ASPgg 68 " --> pdb=" O GLYgg 81 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHEgg 77 " --> pdb=" O SERgg 72 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THRgg 86 " --> pdb=" O SERgg 82 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARGgg 99 " --> pdb=" O LEUgg 89 " (cutoff:3.500A) Processing sheet with id=122, first strand: chain 'gg' and resid 109 through 114 removed outlier: 6.280A pdb=" N GLNgg 119 " --> pdb=" O SERgg 114 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SERgg 124 " --> pdb=" O THRgg 128 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THRgg 128 " --> pdb=" O SERgg 124 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILEgg 129 " --> pdb=" O VALgg 142 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VALgg 142 " --> pdb=" O ILEgg 129 " (cutoff:3.500A) Processing sheet with id=123, first strand: chain 'gg' and resid 153 through 157 removed outlier: 4.292A pdb=" N CYSgg 153 " --> pdb=" O CYSgg 168 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILEgg 164 " --> pdb=" O SERgg 157 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VALgg 174 " --> pdb=" O HISgg 188 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THRgg 186 " --> pdb=" O VALgg 176 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain 'gg' and resid 197 through 200 removed outlier: 3.646A pdb=" N THRgg 197 " --> pdb=" O GLYgg 210 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYRgg 228 " --> pdb=" O LEUgg 218 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain 'gg' and resid 238 through 242 removed outlier: 3.795A pdb=" N ALAgg 238 " --> pdb=" O ALAgg 251 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TRPgg 247 " --> pdb=" O SERgg 242 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain 'gg' and resid 288 through 292 removed outlier: 3.533A pdb=" N SERgg 288 " --> pdb=" O GLYgg 301 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THRgg 297 " --> pdb=" O SERgg 292 " (cutoff:3.500A) Processing sheet with id=127, first strand: chain 'gg' and resid 39 through 42 removed outlier: 3.758A pdb=" N ILEgg 40 " --> pdb=" O LEUgg 59 " (cutoff:3.500A) Processing sheet with id=128, first strand: chain 'gg' and resid 296 through 302 removed outlier: 7.597A pdb=" N GLNgg 296 " --> pdb=" O VALgg 312 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEUgg 306 " --> pdb=" O TYRgg 302 " (cutoff:3.500A) Processing sheet with id=129, first strand: chain 'jj' and resid 75 through 81 removed outlier: 4.153A pdb=" N SERjj 76 " --> pdb=" O ASPjj 91 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRPjj 78 " --> pdb=" O ILEjj 89 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VALjj 87 " --> pdb=" O PHEjj 80 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALAjj 112 " --> pdb=" O GLNjj 147 " (cutoff:3.500A) Processing sheet with id=130, first strand: chain 'jj' and resid 213 through 218 removed outlier: 3.652A pdb=" N TRPjj 214 " --> pdb=" O GLYjj 225 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLYjj 225 " --> pdb=" O TRPjj 214 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALAjj 223 " --> pdb=" O VALjj 216 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARGjj 218 " --> pdb=" O GLYjj 221 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLYjj 221 " --> pdb=" O ARGjj 218 " (cutoff:3.500A) Processing sheet with id=131, first strand: chain 'jj' and resid 246 through 250 removed outlier: 6.547A pdb=" N LEUjj 246 " --> pdb=" O ASPjj 328 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASPjj 328 " --> pdb=" O LEUjj 246 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASNjj 324 " --> pdb=" O LEUjj 250 " (cutoff:3.500A) Processing sheet with id=132, first strand: chain 'jj' and resid 252 through 255 Processing sheet with id=133, first strand: chain 'jj' and resid 366 through 371 Processing sheet with id=134, first strand: chain 'jj' and resid 376 through 379 removed outlier: 3.767A pdb=" N GLUjj 377 " --> pdb=" O ILEjj 401 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALAjj 399 " --> pdb=" O ILEjj 379 " (cutoff:3.500A) 3801 hydrogen bonds defined for protein. 11262 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4470 hydrogen bonds 7610 hydrogen bond angles 0 basepair planarities 1741 basepair parallelities 3017 stacking parallelities Total time for adding SS restraints: 525.27 Time building geometry restraints manager: 81.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 23843 1.31 - 1.44: 95071 1.44 - 1.57: 105873 1.57 - 1.69: 11428 1.69 - 1.82: 694 Bond restraints: 236909 Sorted by residual: bond pdb=" O3' A 52025 " pdb=" P A 52026 " ideal model delta sigma weight residual 1.607 1.240 0.367 1.50e-02 4.44e+03 5.98e+02 bond pdb=" C71 7C4jj 503 " pdb=" C72 7C4jj 503 " ideal model delta sigma weight residual 1.635 1.322 0.313 2.00e-02 2.50e+03 2.46e+02 bond pdb=" C62 7C4jj 503 " pdb=" N15 7C4jj 503 " ideal model delta sigma weight residual 1.571 1.348 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C38 7C4jj 503 " pdb=" N05 7C4jj 503 " ideal model delta sigma weight residual 1.578 1.361 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C60 7C4jj 503 " pdb=" N11 7C4jj 503 " ideal model delta sigma weight residual 1.553 1.347 0.206 2.00e-02 2.50e+03 1.06e+02 ... (remaining 236904 not shown) Histogram of bond angle deviations from ideal: 17.89 - 41.67: 1 41.67 - 65.46: 0 65.46 - 89.24: 0 89.24 - 113.03: 161515 113.03 - 136.81: 185978 Bond angle restraints: 347494 Sorted by residual: angle pdb=" O3' A 52025 " pdb=" P A 52026 " pdb=" OP1 A 52026 " ideal model delta sigma weight residual 108.00 17.89 90.11 3.00e+00 1.11e-01 9.02e+02 angle pdb=" C3' A 52025 " pdb=" O3' A 52025 " pdb=" P A 52026 " ideal model delta sigma weight residual 120.20 99.09 21.11 1.50e+00 4.44e-01 1.98e+02 angle pdb=" O3' A 91835 " pdb=" C3' A 91835 " pdb=" C2' A 91835 " ideal model delta sigma weight residual 109.50 128.24 -18.74 1.50e+00 4.44e-01 1.56e+02 angle pdb=" C4' A 5 47 " pdb=" C3' A 5 47 " pdb=" O3' A 5 47 " ideal model delta sigma weight residual 109.40 124.50 -15.10 1.50e+00 4.44e-01 1.01e+02 angle pdb=" C13 7C4jj 503 " pdb=" C14 7C4jj 503 " pdb=" O03 7C4jj 503 " ideal model delta sigma weight residual 91.55 120.81 -29.26 3.00e+00 1.11e-01 9.51e+01 ... (remaining 347489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 124212 35.97 - 71.95: 5592 71.95 - 107.92: 464 107.92 - 143.90: 78 143.90 - 179.87: 171 Dihedral angle restraints: 130517 sinusoidal: 95507 harmonic: 35010 Sorted by residual: dihedral pdb=" C5' A 91679 " pdb=" C4' A 91679 " pdb=" C3' A 91679 " pdb=" O3' A 91679 " ideal model delta sinusoidal sigma weight residual 147.00 69.22 77.78 1 8.00e+00 1.56e-02 1.18e+02 dihedral pdb=" C5' A 52313 " pdb=" C4' A 52313 " pdb=" C3' A 52313 " pdb=" O3' A 52313 " ideal model delta sinusoidal sigma weight residual 147.00 70.27 76.73 1 8.00e+00 1.56e-02 1.16e+02 dihedral pdb=" C5' U 9 688 " pdb=" C4' U 9 688 " pdb=" C3' U 9 688 " pdb=" O3' U 9 688 " ideal model delta sinusoidal sigma weight residual 147.00 71.25 75.75 1 8.00e+00 1.56e-02 1.13e+02 ... (remaining 130514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 36773 0.148 - 0.296: 6314 0.296 - 0.444: 98 0.444 - 0.592: 33 0.592 - 0.740: 14 Chirality restraints: 43232 Sorted by residual: chirality pdb=" C3' G 51370 " pdb=" C4' G 51370 " pdb=" O3' G 51370 " pdb=" C2' G 51370 " both_signs ideal model delta sigma weight residual False -2.74 -2.00 -0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" C3' C 52266 " pdb=" C4' C 52266 " pdb=" O3' C 52266 " pdb=" C2' C 52266 " both_signs ideal model delta sigma weight residual False -2.74 -2.02 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" C3' G 52089 " pdb=" C4' G 52089 " pdb=" O3' G 52089 " pdb=" C2' G 52089 " both_signs ideal model delta sigma weight residual False -2.74 -2.03 -0.71 2.00e-01 2.50e+01 1.27e+01 ... (remaining 43229 not shown) Planarity restraints: 22645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VALKK 40 " -0.124 5.00e-02 4.00e+02 1.96e-01 6.16e+01 pdb=" N PROKK 41 " 0.339 5.00e-02 4.00e+02 pdb=" CA PROKK 41 " -0.126 5.00e-02 4.00e+02 pdb=" CD PROKK 41 " -0.090 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C 9 585 " -0.084 2.00e-02 2.50e+03 3.83e-02 3.31e+01 pdb=" N1 C 9 585 " 0.039 2.00e-02 2.50e+03 pdb=" C2 C 9 585 " 0.027 2.00e-02 2.50e+03 pdb=" O2 C 9 585 " 0.023 2.00e-02 2.50e+03 pdb=" N3 C 9 585 " -0.011 2.00e-02 2.50e+03 pdb=" C4 C 9 585 " -0.010 2.00e-02 2.50e+03 pdb=" N4 C 9 585 " -0.036 2.00e-02 2.50e+03 pdb=" C5 C 9 585 " 0.013 2.00e-02 2.50e+03 pdb=" C6 C 9 585 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLNXX 61 " 0.095 5.00e-02 4.00e+02 1.42e-01 3.25e+01 pdb=" N PROXX 62 " -0.246 5.00e-02 4.00e+02 pdb=" CA PROXX 62 " 0.082 5.00e-02 4.00e+02 pdb=" CD PROXX 62 " 0.069 5.00e-02 4.00e+02 ... (remaining 22642 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.88: 18 1.88 - 2.63: 4012 2.63 - 3.39: 271458 3.39 - 4.14: 696143 4.14 - 4.90: 1011099 Nonbonded interactions: 1982730 Sorted by model distance: nonbonded pdb=" C3' A 52025 " pdb=" OP1 A 52026 " model vdw 1.121 2.776 nonbonded pdb=" O4 U 91137 " pdb=" N1 A 91148 " model vdw 1.535 2.496 nonbonded pdb=" O4 U 53914 " pdb=" N1 A 54378 " model vdw 1.617 2.496 nonbonded pdb=" N1 A 52367 " pdb=" O4 U 52788 " model vdw 1.663 2.496 nonbonded pdb=" OP2 A 52282 " pdb="MG MG 55132 " model vdw 1.741 2.170 ... (remaining 1982725 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '2' selection = chain 'ii' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 5744 5.49 5 Mg 276 5.21 5 S 442 5.16 5 C 116548 2.51 5 N 41128 2.21 5 O 56788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 32.230 Check model and map are aligned: 2.250 Convert atoms to be neutral: 1.290 Process input model: 950.340 Find NCS groups from input model: 6.080 Set up NCS constraints: 0.640 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 1001.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.367 236909 Z= 0.418 Angle : 1.159 90.115 347494 Z= 0.779 Chirality : 0.096 0.740 43232 Planarity : 0.006 0.225 22645 Dihedral : 18.080 179.869 107949 Min Nonbonded Distance : 1.121 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.95 % Favored : 93.58 % Rotamer Outliers : 6.66 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.06), residues: 11974 helix: -1.07 (0.06), residues: 4018 sheet: -3.20 (0.10), residues: 1831 loop : -2.20 (0.07), residues: 6125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4658 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 694 poor density : 3964 time to evaluate : 11.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 694 outliers final: 148 residues processed: 4362 average time/residue: 2.0581 time to fit residues: 14975.3444 Evaluate side-chains 2754 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 2606 time to evaluate : 10.638 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 148 outliers final: 2 residues processed: 148 average time/residue: 1.6919 time to fit residues: 470.1372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1750 random chunks: chunk 1477 optimal weight: 0.9990 chunk 1326 optimal weight: 8.9990 chunk 736 optimal weight: 7.9990 chunk 453 optimal weight: 0.9990 chunk 894 optimal weight: 8.9990 chunk 708 optimal weight: 6.9990 chunk 1371 optimal weight: 6.9990 chunk 530 optimal weight: 3.9990 chunk 834 optimal weight: 10.0000 chunk 1020 optimal weight: 7.9990 chunk 1589 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 HIS B 167 GLN B 204 GLN B 302 ASN B 328 ASN C 119 GLN C 215 ASN D 81 HIS D 202 GLN E 253 GLN ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN G 99 GLN G 134 ASN ** H 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN H 102 ASN H 156 ASN I 95 HIS I 144 ASN J 23 ASN J 65 ASN J 167 GLN L 28 GLN M 56 GLN N 37 HIS ** N 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 5 GLN O 173 GLN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 ASN P 116 HIS ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 ASN R 36 ASN R 86 ASN R 158 GLN S 125 GLN S 163 HIS T 3 ASN T 69 GLN T 79 GLN T 131 GLN U 41 GLN U 50 ASN V 135 ASN ** Z 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 67 GLN a 120 GLN b 19 ASN b 50 ASN b 60 ASN b 61 ASN c 50 ASN d 30 HIS ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 62 ASN h 107 GLN l 19 GLN l 33 ASN ** o 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 41 ASN r 83 ASN s 41 GLN ** s 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 113 GLN AA 132 GLN AA 141 ASN CC 267 GLN ** CC 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DD 74 GLN EE 17 HIS FF 179 ASN FF 186 ASN GG 4 ASN GG 105 ASN GG 197 GLN HH 91 HIS II 165 GLN JJ 132 GLN KK 28 HIS LL 19 ASN OO 20 GLN ** PP 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** PP 104 GLN ** QQ 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** QQ 97 GLN SS 11 HIS SS 73 ASN TT 126 GLN WW 24 GLN WW 82 GLN WW 98 GLN WW 113 HIS ** XX 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZZ 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** aa 72 HIS ** cc 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ee 110 GLN ff 111 ASN ** gg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** gg 181 ASN gg 196 ASN gg 237 ASN ** gg 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** jj 251 GLN jj 295 HIS jj 367 HIS Total number of N/Q/H flips: 91 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 236909 Z= 0.303 Angle : 0.711 19.469 347494 Z= 0.366 Chirality : 0.043 0.422 43232 Planarity : 0.006 0.154 22645 Dihedral : 16.573 179.965 82463 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer Outliers : 4.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.01 % 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: -1.28 (0.07), residues: 11974 helix: 1.17 (0.08), residues: 4111 sheet: -2.60 (0.10), residues: 1881 loop : -1.73 (0.07), residues: 5982 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3341 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 511 poor density : 2830 time to evaluate : 11.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 511 outliers final: 277 residues processed: 3099 average time/residue: 1.8243 time to fit residues: 9746.6678 Evaluate side-chains 2732 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 2455 time to evaluate : 10.739 Switching outliers to nearest non-outliers outliers start: 277 outliers final: 0 residues processed: 277 average time/residue: 1.4428 time to fit residues: 756.8158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1750 random chunks: chunk 883 optimal weight: 7.9990 chunk 493 optimal weight: 3.9990 chunk 1322 optimal weight: 10.0000 chunk 1082 optimal weight: 10.0000 chunk 438 optimal weight: 0.0870 chunk 1592 optimal weight: 4.9990 chunk 1719 optimal weight: 5.9990 chunk 1417 optimal weight: 1.9990 chunk 1578 optimal weight: 7.9990 chunk 542 optimal weight: 7.9990 chunk 1277 optimal weight: 6.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 HIS D 225 GLN ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN F 109 GLN G 119 GLN H 39 ASN H 78 GLN I 144 ASN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN L 113 ASN L 159 ASN N 37 HIS ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN T 95 HIS U 50 ASN U 94 ASN ** Z 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 76 ASN ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 GLN b 19 ASN b 60 ASN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 80 ASN ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 110 GLN h 107 GLN i 15 HIS l 17 GLN ** o 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 83 ASN ** s 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 195 ASN AA 84 GLN AA 169 HIS CC 178 HIS ** CC 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 17 HIS EE 188 ASN GG 4 ASN HH 163 GLN HH 186 ASN II 99 ASN JJ 132 GLN ** KK 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** KK 50 GLN ** LL 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PP 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** PP 104 GLN ** QQ 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** QQ 48 GLN QQ 97 GLN SS 76 GLN TT 83 GLN TT 126 GLN VV 33 GLN ** WW 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** XX 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZZ 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** aa 17 HIS bb 49 HIS ** cc 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** dd 3 HIS gg 15 ASN ** gg 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** gg 159 ASN ** gg 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** jj 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** jj 251 GLN jj 296 HIS ** jj 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 236909 Z= 0.341 Angle : 0.671 14.228 347494 Z= 0.346 Chirality : 0.041 0.342 43232 Planarity : 0.006 0.153 22645 Dihedral : 16.262 179.296 82463 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.23 % Favored : 95.73 % Rotamer Outliers : 4.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.07), residues: 11974 helix: 1.46 (0.08), residues: 4076 sheet: -2.18 (0.10), residues: 1897 loop : -1.47 (0.07), residues: 6001 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3072 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 421 poor density : 2651 time to evaluate : 10.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 421 outliers final: 201 residues processed: 2903 average time/residue: 1.7380 time to fit residues: 8686.9709 Evaluate side-chains 2598 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 2397 time to evaluate : 10.747 Switching outliers to nearest non-outliers outliers start: 201 outliers final: 0 residues processed: 201 average time/residue: 1.4031 time to fit residues: 545.0714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1750 random chunks: chunk 1572 optimal weight: 6.9990 chunk 1196 optimal weight: 10.0000 chunk 826 optimal weight: 6.9990 chunk 176 optimal weight: 0.4980 chunk 759 optimal weight: 9.9990 chunk 1069 optimal weight: 10.0000 chunk 1597 optimal weight: 3.9990 chunk 1691 optimal weight: 3.9990 chunk 834 optimal weight: 10.0000 chunk 1514 optimal weight: 0.9980 chunk 455 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN C 310 HIS D 111 ASN ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN H 138 GLN L 159 ASN N 37 HIS N 196 ASN ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 72 HIS ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 131 GLN U 50 ASN ** V 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 67 GLN b 19 ASN b 58 GLN c 50 ASN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 80 ASN g 18 ASN h 62 ASN ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 107 GLN j 76 HIS p 72 ASN r 121 GLN s 39 GLN s 41 GLN ** s 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 113 GLN ** CC 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DD 74 GLN DD 226 GLN EE 17 HIS EE 112 HIS FF 179 ASN GG 4 ASN ** GG 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JJ 177 ASN ** NN 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PP 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QQ 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** QQ 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TT 126 GLN WW 56 HIS ** XX 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YY 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** cc 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ff 139 HIS gg 15 ASN ** gg 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** jj 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** jj 108 GLN jj 251 GLN ** jj 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 236909 Z= 0.324 Angle : 0.657 16.000 347494 Z= 0.334 Chirality : 0.040 0.366 43232 Planarity : 0.005 0.151 22645 Dihedral : 16.155 179.992 82463 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.94 % Rotamer Outliers : 3.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.07), residues: 11974 helix: 1.52 (0.08), residues: 4078 sheet: -1.80 (0.11), residues: 1896 loop : -1.34 (0.07), residues: 6000 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2978 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 409 poor density : 2569 time to evaluate : 10.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 409 outliers final: 204 residues processed: 2803 average time/residue: 1.7398 time to fit residues: 8409.2987 Evaluate side-chains 2586 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 2382 time to evaluate : 10.619 Switching outliers to nearest non-outliers outliers start: 204 outliers final: 0 residues processed: 204 average time/residue: 1.3853 time to fit residues: 548.1308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1750 random chunks: chunk 1408 optimal weight: 0.9980 chunk 960 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 1259 optimal weight: 3.9990 chunk 697 optimal weight: 8.9990 chunk 1443 optimal weight: 10.0000 chunk 1169 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 863 optimal weight: 6.9990 chunk 1518 optimal weight: 0.9980 chunk 426 optimal weight: 0.4980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN G 161 GLN G 248 HIS I 59 GLN J 23 ASN J 167 GLN L 159 ASN L 188 ASN N 37 HIS ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN ** V 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 96 GLN ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 19 ASN b 60 ASN b 61 ASN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 HIS s 41 GLN s 68 HIS ** t 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 141 ASN CC 272 HIS EE 17 HIS FF 36 GLN FF 137 GLN GG 4 ASN ** GG 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HH 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JJ 177 ASN ** PP 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PP 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** QQ 24 HIS QQ 86 GLN ** XX 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YY 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** bb 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** cc 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** gg 222 ASN ** jj 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** jj 108 GLN jj 251 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 236909 Z= 0.226 Angle : 0.598 16.371 347494 Z= 0.304 Chirality : 0.037 0.295 43232 Planarity : 0.005 0.149 22645 Dihedral : 16.012 179.962 82463 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.02 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.07), residues: 11974 helix: 1.60 (0.08), residues: 4085 sheet: -1.56 (0.11), residues: 1908 loop : -1.21 (0.07), residues: 5981 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2780 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 2514 time to evaluate : 12.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 266 outliers final: 137 residues processed: 2656 average time/residue: 1.8692 time to fit residues: 8595.6396 Evaluate side-chains 2500 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 2363 time to evaluate : 10.670 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 0 residues processed: 137 average time/residue: 1.5225 time to fit residues: 404.6336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1750 random chunks: chunk 569 optimal weight: 3.9990 chunk 1523 optimal weight: 8.9990 chunk 334 optimal weight: 0.7980 chunk 993 optimal weight: 6.9990 chunk 417 optimal weight: 6.9990 chunk 1693 optimal weight: 0.0030 chunk 1405 optimal weight: 0.8980 chunk 783 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 560 optimal weight: 3.9990 chunk 888 optimal weight: 10.0000 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 ASN P 21 ASN Q 8 ASN R 34 ASN R 86 ASN T 98 HIS T 131 GLN U 41 GLN ** V 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 GLN Y 86 GLN ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 67 GLN b 19 ASN b 60 ASN ** b 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 50 ASN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 ASN h 62 ASN r 70 GLN s 68 HIS ** t 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 169 HIS ** EE 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EE 157 ASN FF 137 GLN ** GG 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HH 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JJ 177 ASN LL 108 ASN ** PP 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** WW 98 GLN YY 94 HIS ** cc 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** gg 159 ASN gg 296 GLN ** jj 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** jj 251 GLN ** jj 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.087 236909 Z= 0.174 Angle : 0.568 14.960 347494 Z= 0.288 Chirality : 0.035 0.391 43232 Planarity : 0.005 0.147 22645 Dihedral : 15.882 179.626 82463 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.43 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.08), residues: 11974 helix: 1.70 (0.08), residues: 4080 sheet: -1.37 (0.11), residues: 1935 loop : -1.10 (0.08), residues: 5959 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2738 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 2516 time to evaluate : 10.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 222 outliers final: 115 residues processed: 2622 average time/residue: 1.7471 time to fit residues: 7932.4367 Evaluate side-chains 2476 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 2361 time to evaluate : 10.584 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 0 residues processed: 115 average time/residue: 1.3855 time to fit residues: 315.5223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1750 random chunks: chunk 1632 optimal weight: 0.0470 chunk 190 optimal weight: 0.0570 chunk 964 optimal weight: 7.9990 chunk 1236 optimal weight: 9.9990 chunk 958 optimal weight: 8.9990 chunk 1425 optimal weight: 9.9990 chunk 945 optimal weight: 10.0000 chunk 1686 optimal weight: 9.9990 chunk 1055 optimal weight: 10.0000 chunk 1028 optimal weight: 10.0000 chunk 778 optimal weight: 20.0000 overall best weight: 5.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 GLN ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN L 149 GLN L 159 ASN N 196 ASN ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN Q 125 GLN R 34 ASN U 41 GLN U 50 ASN ** V 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 86 GLN ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 19 ASN b 60 ASN b 61 ASN ** b 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 17 HIS FF 137 GLN GG 4 ASN ** GG 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HH 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JJ 177 ASN KK 7 ASN MM 28 HIS OO 32 HIS ** PP 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QQ 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TT 85 ASN WW 92 ASN bb 26 GLN ** cc 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** dd 28 HIS ** gg 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** jj 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** jj 108 GLN jj 251 GLN ** jj 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** jj 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.122 236909 Z= 0.518 Angle : 0.750 17.289 347494 Z= 0.377 Chirality : 0.045 0.409 43232 Planarity : 0.006 0.148 22645 Dihedral : 16.060 179.750 82463 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.82 % Favored : 95.14 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.07), residues: 11974 helix: 1.26 (0.08), residues: 4085 sheet: -1.45 (0.11), residues: 1879 loop : -1.23 (0.07), residues: 6010 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2676 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 2394 time to evaluate : 12.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 282 outliers final: 168 residues processed: 2520 average time/residue: 1.7699 time to fit residues: 7714.4990 Evaluate side-chains 2474 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 2306 time to evaluate : 10.629 Switching outliers to nearest non-outliers outliers start: 168 outliers final: 0 residues processed: 168 average time/residue: 1.4203 time to fit residues: 463.1114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1750 random chunks: chunk 1043 optimal weight: 7.9990 chunk 673 optimal weight: 20.0000 chunk 1007 optimal weight: 7.9990 chunk 508 optimal weight: 5.9990 chunk 331 optimal weight: 1.9990 chunk 326 optimal weight: 0.8980 chunk 1072 optimal weight: 10.0000 chunk 1149 optimal weight: 4.9990 chunk 833 optimal weight: 20.0000 chunk 157 optimal weight: 0.7980 chunk 1325 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN E 214 HIS ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN J 23 ASN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN ** J 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN N 37 HIS N 196 ASN ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 ASN P 21 ASN Q 77 ASN Q 125 GLN T 131 GLN U 50 ASN ** V 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 96 GLN W 104 GLN Y 86 GLN ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 60 ASN ** b 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 62 ASN m 61 GLN s 68 HIS ** t 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DD 74 GLN GG 4 ASN ** GG 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JJ 177 ASN KK 7 ASN OO 32 HIS ** PP 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QQ 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** VV 21 ASN WW 92 ASN ** cc 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** jj 108 GLN jj 251 GLN ** jj 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.672 236909 Z= 0.339 Angle : 0.641 38.945 347494 Z= 0.325 Chirality : 0.038 0.386 43232 Planarity : 0.005 0.148 22645 Dihedral : 15.954 179.977 82463 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.04 % Favored : 95.92 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.07), residues: 11974 helix: 1.34 (0.08), residues: 4086 sheet: -1.38 (0.11), residues: 1892 loop : -1.18 (0.07), residues: 5996 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2566 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 2405 time to evaluate : 10.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 161 outliers final: 90 residues processed: 2483 average time/residue: 1.8609 time to fit residues: 8017.8847 Evaluate side-chains 2417 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 2327 time to evaluate : 10.647 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 0 residues processed: 90 average time/residue: 1.5066 time to fit residues: 268.3420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1750 random chunks: chunk 1534 optimal weight: 5.9990 chunk 1615 optimal weight: 6.9990 chunk 1474 optimal weight: 5.9990 chunk 1571 optimal weight: 9.9990 chunk 946 optimal weight: 20.0000 chunk 684 optimal weight: 6.9990 chunk 1234 optimal weight: 5.9990 chunk 482 optimal weight: 4.9990 chunk 1420 optimal weight: 0.9990 chunk 1486 optimal weight: 0.9990 chunk 1566 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN ** J 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN N 37 HIS ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 131 GLN U 50 ASN ** V 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 19 ASN b 60 ASN b 61 ASN ** b 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 12 ASN r 36 ASN ** s 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 169 HIS GG 4 ASN ** GG 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JJ 177 ASN KK 7 ASN OO 32 HIS ** PP 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QQ 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** WW 92 ASN ** cc 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** jj 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.249 236909 Z= 0.342 Angle : 0.658 19.071 347494 Z= 0.333 Chirality : 0.039 0.337 43232 Planarity : 0.005 0.146 22645 Dihedral : 15.936 179.911 82463 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.07), residues: 11974 helix: 1.26 (0.08), residues: 4082 sheet: -1.35 (0.11), residues: 1888 loop : -1.18 (0.07), residues: 6004 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2497 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 2360 time to evaluate : 10.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 137 outliers final: 78 residues processed: 2427 average time/residue: 1.7501 time to fit residues: 7344.2900 Evaluate side-chains 2370 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 2292 time to evaluate : 11.778 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 0 residues processed: 78 average time/residue: 1.5482 time to fit residues: 243.3694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1750 random chunks: chunk 1032 optimal weight: 7.9990 chunk 1662 optimal weight: 9.9990 chunk 1014 optimal weight: 10.0000 chunk 788 optimal weight: 5.9990 chunk 1155 optimal weight: 8.9990 chunk 1743 optimal weight: 1.9990 chunk 1604 optimal weight: 0.6980 chunk 1388 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 1072 optimal weight: 10.0000 chunk 851 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN L 159 ASN ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 ASN P 21 ASN Q 77 ASN R 34 ASN T 131 GLN ** V 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 19 ASN b 60 ASN ** b 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 50 ASN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 62 ASN r 36 ASN ** s 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EE 157 ASN FF 179 ASN GG 4 ASN ** GG 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HH 163 GLN II 99 ASN ** II 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JJ 177 ASN KK 7 ASN OO 32 HIS QQ 86 GLN UU 92 HIS WW 92 ASN ** ZZ 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** cc 29 GLN gg 15 ASN ** gg 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** jj 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.517 236909 Z= 0.339 Angle : 0.655 28.499 347494 Z= 0.331 Chirality : 0.039 0.312 43232 Planarity : 0.005 0.144 22645 Dihedral : 15.921 179.934 82463 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.42 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.01 % 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: -0.56 (0.07), residues: 11974 helix: 1.23 (0.08), residues: 4091 sheet: -1.32 (0.11), residues: 1893 loop : -1.18 (0.08), residues: 5990 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23948 Ramachandran restraints generated. 11974 Oldfield, 0 Emsley, 11974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2447 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 2372 time to evaluate : 10.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 49 residues processed: 2400 average time/residue: 1.8952 time to fit residues: 7901.9120 Evaluate side-chains 2357 residues out of total 10422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 2308 time to evaluate : 11.613 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 1.4403 time to fit residues: 145.6627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1750 random chunks: chunk 1102 optimal weight: 10.0000 chunk 1478 optimal weight: 0.8980 chunk 425 optimal weight: 6.9990 chunk 1280 optimal weight: 0.9980 chunk 204 optimal weight: 0.4980 chunk 385 optimal weight: 2.9990 chunk 1390 optimal weight: 0.8980 chunk 581 optimal weight: 0.7980 chunk 1427 optimal weight: 0.5980 chunk 176 optimal weight: 0.6980 chunk 256 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN D 191 ASN D 282 GLN ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN J 167 GLN L 159 ASN ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN R 34 ASN S 146 HIS T 112 ASN X 107 HIS a 28 HIS ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 19 ASN b 60 ASN b 61 ASN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 12 ASN r 36 ASN s 191 GLN ** t 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EE 157 ASN ** GG 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HH 163 GLN II 99 ASN ** II 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JJ 177 ASN KK 7 ASN OO 32 HIS WW 92 ASN WW 98 GLN ** gg 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** gg 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** jj 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** jj 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.101303 restraints weight = 352581.392| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.19 r_work: 0.3067 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 1.13 restraints_weight: 0.2500 r_work: 0.3047 rms_B_bonded: 1.21 restraints_weight: 0.1250 r_work: 0.3036 rms_B_bonded: 1.32 restraints_weight: 0.0625 r_work: 0.3025 rms_B_bonded: 1.46 restraints_weight: 0.0312 r_work: 0.3013 rms_B_bonded: 1.64 restraints_weight: 0.0156 r_work: 0.2999 rms_B_bonded: 1.85 restraints_weight: 0.0078 r_work: 0.2984 rms_B_bonded: 2.10 restraints_weight: 0.0039 r_work: 0.2968 rms_B_bonded: 2.39 restraints_weight: 0.0020 r_work: 0.2950 rms_B_bonded: 2.72 restraints_weight: 0.0010 r_work: 0.2930 rms_B_bonded: 3.10 restraints_weight: 0.0005 r_work: 0.2907 rms_B_bonded: 3.55 restraints_weight: 0.0002 r_work: 0.2882 rms_B_bonded: 4.06 restraints_weight: 0.0001 r_work: 0.2854 rms_B_bonded: 4.66 restraints_weight: 0.0001 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.411 236909 Z= 0.161 Angle : 0.577 16.872 347494 Z= 0.292 Chirality : 0.034 0.277 43232 Planarity : 0.005 0.143 22645 Dihedral : 15.766 179.892 82463 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.23 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.08), residues: 11974 helix: 1.47 (0.08), residues: 4095 sheet: -1.18 (0.11), residues: 1876 loop : -1.02 (0.08), residues: 6003 =============================================================================== Job complete usr+sys time: 106346.82 seconds wall clock time: 1824 minutes 22.05 seconds (109462.05 seconds total)