Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 10:13:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mp9_3534/04_2023/5mp9_3534_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mp9_3534/04_2023/5mp9_3534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mp9_3534/04_2023/5mp9_3534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mp9_3534/04_2023/5mp9_3534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mp9_3534/04_2023/5mp9_3534_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mp9_3534/04_2023/5mp9_3534_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 6 5.21 5 S 245 5.16 5 C 42802 2.51 5 N 11637 2.21 5 O 13176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a GLU 20": "OE1" <-> "OE2" Residue "a GLU 168": "OE1" <-> "OE2" Residue "a GLU 174": "OE1" <-> "OE2" Residue "a GLU 187": "OE1" <-> "OE2" Residue "a GLU 188": "OE1" <-> "OE2" Residue "a GLU 195": "OE1" <-> "OE2" Residue "a GLU 208": "OE1" <-> "OE2" Residue "a GLU 215": "OE1" <-> "OE2" Residue "a GLU 230": "OE1" <-> "OE2" Residue "a GLU 233": "OE1" <-> "OE2" Residue "a GLU 234": "OE1" <-> "OE2" Residue "a GLU 241": "OE1" <-> "OE2" Residue "b GLU 48": "OE1" <-> "OE2" Residue "b GLU 59": "OE1" <-> "OE2" Residue "b GLU 141": "OE1" <-> "OE2" Residue "b GLU 182": "OE1" <-> "OE2" Residue "b GLU 184": "OE1" <-> "OE2" Residue "b GLU 198": "OE1" <-> "OE2" Residue "b GLU 210": "OE1" <-> "OE2" Residue "b GLU 248": "OE1" <-> "OE2" Residue "c GLU 15": "OE1" <-> "OE2" Residue "c GLU 22": "OE1" <-> "OE2" Residue "c GLU 26": "OE1" <-> "OE2" Residue "c GLU 57": "OE1" <-> "OE2" Residue "c GLU 108": "OE1" <-> "OE2" Residue "c ARG 112": "NH1" <-> "NH2" Residue "c GLU 233": "OE1" <-> "OE2" Residue "d GLU 19": "OE1" <-> "OE2" Residue "d GLU 90": "OE1" <-> "OE2" Residue "d GLU 105": "OE1" <-> "OE2" Residue "d ARG 109": "NH1" <-> "NH2" Residue "d GLU 142": "OE1" <-> "OE2" Residue "d GLU 149": "OE1" <-> "OE2" Residue "d ARG 164": "NH1" <-> "NH2" Residue "d GLU 171": "OE1" <-> "OE2" Residue "d GLU 199": "OE1" <-> "OE2" Residue "d GLU 225": "OE1" <-> "OE2" Residue "d GLU 235": "OE1" <-> "OE2" Residue "d GLU 237": "OE1" <-> "OE2" Residue "d GLU 240": "OE1" <-> "OE2" Residue "e GLU 10": "OE1" <-> "OE2" Residue "e GLU 17": "OE1" <-> "OE2" Residue "e GLU 21": "OE1" <-> "OE2" Residue "e GLU 36": "OE1" <-> "OE2" Residue "e GLU 52": "OE1" <-> "OE2" Residue "e ARG 64": "NH1" <-> "NH2" Residue "e GLU 122": "OE1" <-> "OE2" Residue "e GLU 169": "OE1" <-> "OE2" Residue "e GLU 202": "OE1" <-> "OE2" Residue "e GLU 206": "OE1" <-> "OE2" Residue "e GLU 226": "OE1" <-> "OE2" Residue "e GLU 234": "OE1" <-> "OE2" Residue "e GLU 237": "OE1" <-> "OE2" Residue "e GLU 239": "OE1" <-> "OE2" Residue "f GLU 22": "OE1" <-> "OE2" Residue "f GLU 26": "OE1" <-> "OE2" Residue "f GLU 54": "OE1" <-> "OE2" Residue "f GLU 67": "OE1" <-> "OE2" Residue "f GLU 154": "OE1" <-> "OE2" Residue "f GLU 172": "OE1" <-> "OE2" Residue "f GLU 203": "OE1" <-> "OE2" Residue "g GLU 21": "OE1" <-> "OE2" Residue "g GLU 28": "OE1" <-> "OE2" Residue "g GLU 47": "OE1" <-> "OE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g GLU 91": "OE1" <-> "OE2" Residue "g GLU 148": "OE1" <-> "OE2" Residue "g GLU 211": "OE1" <-> "OE2" Residue "g GLU 234": "OE1" <-> "OE2" Residue "h GLU 84": "OE1" <-> "OE2" Residue "h GLU 144": "OE1" <-> "OE2" Residue "h GLU 149": "OE1" <-> "OE2" Residue "h GLU 150": "OE1" <-> "OE2" Residue "h GLU 194": "OE1" <-> "OE2" Residue "i GLU 53": "OE1" <-> "OE2" Residue "i GLU 64": "OE1" <-> "OE2" Residue "i GLU 139": "OE1" <-> "OE2" Residue "i GLU 150": "OE1" <-> "OE2" Residue "i GLU 179": "OE1" <-> "OE2" Residue "i GLU 197": "OE1" <-> "OE2" Residue "i GLU 198": "OE1" <-> "OE2" Residue "j GLU 64": "OE1" <-> "OE2" Residue "j GLU 96": "OE1" <-> "OE2" Residue "j ARG 98": "NH1" <-> "NH2" Residue "j GLU 154": "OE1" <-> "OE2" Residue "j GLU 160": "OE1" <-> "OE2" Residue "j GLU 164": "OE1" <-> "OE2" Residue "k ARG 23": "NH1" <-> "NH2" Residue "k GLU 74": "OE1" <-> "OE2" Residue "k GLU 156": "OE1" <-> "OE2" Residue "k GLU 167": "OE1" <-> "OE2" Residue "k GLU 169": "OE1" <-> "OE2" Residue "l GLU 70": "OE1" <-> "OE2" Residue "l GLU 108": "OE1" <-> "OE2" Residue "l ARG 121": "NH1" <-> "NH2" Residue "l GLU 182": "OE1" <-> "OE2" Residue "l GLU 195": "OE1" <-> "OE2" Residue "l GLU 204": "OE1" <-> "OE2" Residue "m ARG 28": "NH1" <-> "NH2" Residue "m GLU 116": "OE1" <-> "OE2" Residue "m GLU 134": "OE1" <-> "OE2" Residue "m GLU 161": "OE1" <-> "OE2" Residue "m GLU 179": "OE1" <-> "OE2" Residue "m GLU 203": "OE1" <-> "OE2" Residue "n GLU 40": "OE1" <-> "OE2" Residue "n GLU 64": "OE1" <-> "OE2" Residue "n GLU 73": "OE1" <-> "OE2" Residue "n GLU 174": "OE1" <-> "OE2" Residue "n GLU 175": "OE1" <-> "OE2" Residue "n ARG 182": "NH1" <-> "NH2" Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "E PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 102": "OE1" <-> "OE2" Residue "E PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 123": "OE1" <-> "OE2" Residue "E TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "E GLU 206": "OE1" <-> "OE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E GLU 239": "OE1" <-> "OE2" Residue "E GLU 242": "OE1" <-> "OE2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "G TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 181": "OE1" <-> "OE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "G GLU 209": "OE1" <-> "OE2" Residue "G GLU 234": "OE1" <-> "OE2" Residue "G GLU 242": "OE1" <-> "OE2" Residue "1 ASP 17": "OD1" <-> "OD2" Residue "1 PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 84": "OE1" <-> "OE2" Residue "1 TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 144": "OE1" <-> "OE2" Residue "1 GLU 149": "OE1" <-> "OE2" Residue "1 GLU 192": "OE1" <-> "OE2" Residue "2 GLU 73": "OE1" <-> "OE2" Residue "2 TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 150": "OE1" <-> "OE2" Residue "2 GLU 185": "OE1" <-> "OE2" Residue "2 GLU 198": "OE1" <-> "OE2" Residue "2 GLU 226": "OE1" <-> "OE2" Residue "3 GLU 40": "OE1" <-> "OE2" Residue "3 GLU 64": "OE1" <-> "OE2" Residue "3 GLU 78": "OE1" <-> "OE2" Residue "3 ARG 98": "NH1" <-> "NH2" Residue "3 PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 164": "OE1" <-> "OE2" Residue "3 TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 23": "NH1" <-> "NH2" Residue "4 GLU 49": "OE1" <-> "OE2" Residue "4 GLU 71": "OE1" <-> "OE2" Residue "4 GLU 87": "OE1" <-> "OE2" Residue "4 TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 127": "OE1" <-> "OE2" Residue "4 PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 108": "OE1" <-> "OE2" Residue "5 ARG 121": "NH1" <-> "NH2" Residue "5 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 195": "OE1" <-> "OE2" Residue "5 GLU 202": "OE1" <-> "OE2" Residue "5 GLU 203": "OE1" <-> "OE2" Residue "6 ARG 28": "NH1" <-> "NH2" Residue "6 TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "6 TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 134": "OE1" <-> "OE2" Residue "6 GLU 161": "OE1" <-> "OE2" Residue "6 GLU 178": "OE1" <-> "OE2" Residue "6 GLU 179": "OE1" <-> "OE2" Residue "6 GLU 203": "OE1" <-> "OE2" Residue "6 GLU 215": "OE1" <-> "OE2" Residue "7 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 40": "OE1" <-> "OE2" Residue "7 GLU 84": "OE1" <-> "OE2" Residue "7 PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 162": "OE1" <-> "OE2" Residue "7 GLU 175": "OE1" <-> "OE2" Residue "7 ARG 182": "NH1" <-> "NH2" Residue "7 PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "H TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 161": "OE1" <-> "OE2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H GLU 184": "OE1" <-> "OE2" Residue "H GLU 202": "OE1" <-> "OE2" Residue "H GLU 219": "OE1" <-> "OE2" Residue "H GLU 310": "OE1" <-> "OE2" Residue "H GLU 328": "OE1" <-> "OE2" Residue "H GLU 399": "OE1" <-> "OE2" Residue "H GLU 418": "OE1" <-> "OE2" Residue "H GLU 425": "OE1" <-> "OE2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "I GLU 72": "OE1" <-> "OE2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I GLU 98": "OE1" <-> "OE2" Residue "I GLU 179": "OE1" <-> "OE2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "I GLU 193": "OE1" <-> "OE2" Residue "I GLU 206": "OE1" <-> "OE2" Residue "I GLU 210": "OE1" <-> "OE2" Residue "I TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 273": "OE1" <-> "OE2" Residue "I GLU 351": "OE1" <-> "OE2" Residue "I GLU 373": "OE1" <-> "OE2" Residue "I GLU 398": "OE1" <-> "OE2" Residue "I GLU 414": "OE1" <-> "OE2" Residue "I GLU 430": "OE1" <-> "OE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K GLU 65": "OE1" <-> "OE2" Residue "K GLU 101": "OE1" <-> "OE2" Residue "K GLU 165": "OE1" <-> "OE2" Residue "K ASP 178": "OD1" <-> "OD2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "K TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 241": "OE1" <-> "OE2" Residue "K GLU 291": "OE1" <-> "OE2" Residue "K GLU 348": "OE1" <-> "OE2" Residue "K GLU 365": "OE1" <-> "OE2" Residue "K GLU 389": "OE1" <-> "OE2" Residue "K GLU 408": "OE1" <-> "OE2" Residue "K GLU 409": "OE1" <-> "OE2" Residue "L GLU 49": "OE1" <-> "OE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L GLU 66": "OE1" <-> "OE2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "L GLU 114": "OE1" <-> "OE2" Residue "L GLU 162": "OE1" <-> "OE2" Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 198": "OE1" <-> "OE2" Residue "L GLU 205": "OE1" <-> "OE2" Residue "L TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 272": "OE1" <-> "OE2" Residue "L GLU 307": "OE1" <-> "OE2" Residue "L PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 29": "OE1" <-> "OE2" Residue "M TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 84": "OE1" <-> "OE2" Residue "M GLU 178": "OE1" <-> "OE2" Residue "M TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 282": "OE1" <-> "OE2" Residue "M GLU 354": "OE1" <-> "OE2" Residue "M GLU 413": "OE1" <-> "OE2" Residue "M ARG 425": "NH1" <-> "NH2" Residue "M PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 67": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 165": "OE1" <-> "OE2" Residue "J GLU 172": "OE1" <-> "OE2" Residue "J GLU 175": "OE1" <-> "OE2" Residue "J GLU 225": "OE1" <-> "OE2" Residue "J GLU 232": "OE1" <-> "OE2" Residue "J PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 306": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 67883 Number of models: 1 Model: "" Number of chains: 40 Chain: "a" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1907 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "b" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1915 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain: "c" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1904 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "d" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1881 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 10, 'TRANS': 229} Chain: "e" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1861 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "f" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1773 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain: "g" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1892 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "h" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1512 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "i" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1719 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "j" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1581 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "k" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1561 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "l" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1644 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain: "m" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1757 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "n" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1815 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 8, 'TRANS': 223} Chain: "A" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1907 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1915 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain: "C" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1904 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "D" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1881 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 10, 'TRANS': 229} Chain: "E" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1861 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "F" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1795 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain: "G" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1892 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "1" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1512 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "2" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1719 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "3" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1581 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "4" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1561 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "5" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1644 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain: "6" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1757 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "7" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1790 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "H" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3053 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 368} Chain breaks: 1 Chain: "I" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3022 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 367} Chain: "K" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3078 Classifications: {'peptide': 389} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 371} Chain: "L" Number of atoms: 3082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3082 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 370} Chain: "M" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2986 Classifications: {'peptide': 381} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 365} Chain breaks: 1 Chain: "J" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3033 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 369} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.51, per 1000 atoms: 0.38 Number of scatterers: 67883 At special positions: 0 Unit cell: (291.18, 172.5, 186.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 245 16.00 P 17 15.00 Mg 6 11.99 O 13176 8.00 N 11637 7.00 C 42802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.09 Conformation dependent library (CDL) restraints added in 8.1 seconds 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16006 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 239 helices and 81 sheets defined 37.1% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.64 Creating SS restraints... Processing helix chain 'a' and resid 17 through 26 removed outlier: 3.535A pdb=" N PHE a 23 " --> pdb=" O VAL a 19 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 78 through 99 removed outlier: 3.610A pdb=" N ARG a 96 " --> pdb=" O ALA a 92 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 121 removed outlier: 3.899A pdb=" N TYR a 119 " --> pdb=" O LEU a 115 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR a 120 " --> pdb=" O SER a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 166 through 180 Processing helix chain 'a' and resid 191 through 205 Processing helix chain 'a' and resid 229 through 241 removed outlier: 3.527A pdb=" N ARG a 235 " --> pdb=" O ASN a 231 " (cutoff:3.500A) Processing helix chain 'b' and resid 19 through 30 Processing helix chain 'b' and resid 79 through 97 removed outlier: 3.539A pdb=" N LEU b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS b 94 " --> pdb=" O ARG b 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER b 96 " --> pdb=" O VAL b 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 123 removed outlier: 3.735A pdb=" N SER b 112 " --> pdb=" O LYS b 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 168 through 178 removed outlier: 3.565A pdb=" N THR b 173 " --> pdb=" O VAL b 169 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE b 174 " --> pdb=" O ALA b 170 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS b 177 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG b 178 " --> pdb=" O PHE b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 185 through 199 removed outlier: 4.016A pdb=" N SER b 199 " --> pdb=" O THR b 195 " (cutoff:3.500A) Processing helix chain 'b' and resid 240 through 248 removed outlier: 3.541A pdb=" N ASN b 244 " --> pdb=" O SER b 240 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP b 245 " --> pdb=" O GLN b 241 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG b 246 " --> pdb=" O GLU b 242 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU b 247 " --> pdb=" O ILE b 243 " (cutoff:3.500A) Processing helix chain 'c' and resid 19 through 29 Processing helix chain 'c' and resid 80 through 101 removed outlier: 3.844A pdb=" N ILE c 85 " --> pdb=" O ALA c 81 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN c 88 " --> pdb=" O GLU c 84 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 123 removed outlier: 3.901A pdb=" N LEU c 114 " --> pdb=" O LEU c 110 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR c 121 " --> pdb=" O ILE c 117 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR c 122 " --> pdb=" O LYS c 118 " (cutoff:3.500A) Processing helix chain 'c' and resid 168 through 178 Processing helix chain 'c' and resid 185 through 198 removed outlier: 3.718A pdb=" N LYS c 198 " --> pdb=" O LYS c 194 " (cutoff:3.500A) Processing helix chain 'c' and resid 207 through 209 No H-bonds generated for 'chain 'c' and resid 207 through 209' Processing helix chain 'c' and resid 231 through 240 removed outlier: 3.689A pdb=" N LYS c 235 " --> pdb=" O PRO c 231 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP c 236 " --> pdb=" O GLN c 232 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 27 removed outlier: 3.504A pdb=" N GLU d 23 " --> pdb=" O GLU d 19 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG d 27 " --> pdb=" O GLU d 23 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 97 removed outlier: 3.666A pdb=" N ARG d 81 " --> pdb=" O ASN d 77 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU d 83 " --> pdb=" O ASP d 79 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU d 85 " --> pdb=" O ARG d 81 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG d 95 " --> pdb=" O ALA d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 104 through 119 removed outlier: 3.503A pdb=" N THR d 108 " --> pdb=" O VAL d 104 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR d 118 " --> pdb=" O VAL d 114 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) Processing helix chain 'd' and resid 166 through 176 removed outlier: 3.719A pdb=" N LYS d 175 " --> pdb=" O GLU d 171 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 199 removed outlier: 3.798A pdb=" N GLU d 199 " --> pdb=" O ARG d 195 " (cutoff:3.500A) Processing helix chain 'd' and resid 224 through 238 removed outlier: 3.595A pdb=" N TYR d 230 " --> pdb=" O GLU d 226 " (cutoff:3.500A) Processing helix chain 'e' and resid 14 through 22 Processing helix chain 'e' and resid 74 through 94 removed outlier: 3.740A pdb=" N ARG e 78 " --> pdb=" O THR e 74 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N SER e 79 " --> pdb=" O ALA e 75 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET e 80 " --> pdb=" O ASP e 76 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 113 removed outlier: 3.899A pdb=" N LEU e 111 " --> pdb=" O SER e 107 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA e 112 " --> pdb=" O VAL e 108 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU e 113 " --> pdb=" O CYS e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 168 through 178 removed outlier: 4.047A pdb=" N ASN e 177 " --> pdb=" O ALA e 173 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU e 178 " --> pdb=" O GLU e 174 " (cutoff:3.500A) Processing helix chain 'e' and resid 185 through 199 removed outlier: 3.544A pdb=" N GLN e 198 " --> pdb=" O LYS e 194 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL e 199 " --> pdb=" O ILE e 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 225 through 241 removed outlier: 3.802A pdb=" N GLU e 230 " --> pdb=" O GLU e 226 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU e 231 " --> pdb=" O LYS e 227 " (cutoff:3.500A) Processing helix chain 'f' and resid 19 through 30 removed outlier: 4.114A pdb=" N ILE f 28 " --> pdb=" O ALA f 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS f 29 " --> pdb=" O LEU f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 77 through 97 removed outlier: 3.533A pdb=" N VAL f 82 " --> pdb=" O PRO f 78 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR f 86 " --> pdb=" O VAL f 82 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN f 90 " --> pdb=" O TYR f 86 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 120 removed outlier: 3.603A pdb=" N HIS f 109 " --> pdb=" O GLU f 105 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN f 118 " --> pdb=" O LYS f 114 " (cutoff:3.500A) Processing helix chain 'f' and resid 164 through 178 removed outlier: 3.712A pdb=" N THR f 169 " --> pdb=" O GLY f 166 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU f 171 " --> pdb=" O LYS f 168 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR f 174 " --> pdb=" O LEU f 171 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU f 175 " --> pdb=" O GLU f 172 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP f 176 " --> pdb=" O ARG f 173 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE f 178 " --> pdb=" O LEU f 175 " (cutoff:3.500A) Processing helix chain 'f' and resid 185 through 197 Processing helix chain 'f' and resid 226 through 229 removed outlier: 3.522A pdb=" N VAL f 229 " --> pdb=" O GLY f 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 226 through 229' Processing helix chain 'g' and resid 18 through 29 removed outlier: 3.683A pdb=" N LYS g 25 " --> pdb=" O GLU g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 78 through 98 removed outlier: 3.613A pdb=" N GLU g 90 " --> pdb=" O ASN g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 105 through 120 removed outlier: 3.856A pdb=" N ASP g 110 " --> pdb=" O PRO g 106 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU g 112 " --> pdb=" O PHE g 108 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N HIS g 119 " --> pdb=" O TYR g 115 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR g 120 " --> pdb=" O VAL g 116 " (cutoff:3.500A) Processing helix chain 'g' and resid 163 through 177 removed outlier: 4.546A pdb=" N GLN g 166 " --> pdb=" O LYS g 163 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER g 167 " --> pdb=" O GLY g 164 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS g 169 " --> pdb=" O GLN g 166 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU g 172 " --> pdb=" O LYS g 169 " (cutoff:3.500A) Processing helix chain 'g' and resid 185 through 201 removed outlier: 3.724A pdb=" N VAL g 189 " --> pdb=" O ALA g 185 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS g 190 " --> pdb=" O ARG g 186 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA g 193 " --> pdb=" O VAL g 189 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU g 201 " --> pdb=" O TYR g 197 " (cutoff:3.500A) Processing helix chain 'g' and resid 230 through 243 Processing helix chain 'h' and resid 49 through 70 removed outlier: 3.503A pdb=" N GLU h 64 " --> pdb=" O GLN h 60 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER h 68 " --> pdb=" O GLU h 64 " (cutoff:3.500A) Processing helix chain 'h' and resid 75 through 88 Processing helix chain 'h' and resid 132 through 141 removed outlier: 3.504A pdb=" N TYR h 135 " --> pdb=" O THR h 132 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLY h 136 " --> pdb=" O PHE h 133 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS h 138 " --> pdb=" O TYR h 135 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS h 140 " --> pdb=" O TYR h 137 " (cutoff:3.500A) Processing helix chain 'h' and resid 148 through 165 removed outlier: 3.823A pdb=" N ASP h 153 " --> pdb=" O GLU h 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 190 through 193 No H-bonds generated for 'chain 'h' and resid 190 through 193' Processing helix chain 'i' and resid 49 through 70 removed outlier: 3.506A pdb=" N GLU i 53 " --> pdb=" O ALA i 49 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN i 57 " --> pdb=" O GLU i 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE i 59 " --> pdb=" O VAL i 55 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN i 62 " --> pdb=" O LEU i 58 " (cutoff:3.500A) Processing helix chain 'i' and resid 76 through 88 removed outlier: 3.623A pdb=" N GLN i 85 " --> pdb=" O GLN i 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 131 through 141 removed outlier: 3.696A pdb=" N VAL i 137 " --> pdb=" O ALA i 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS i 141 " --> pdb=" O VAL i 137 " (cutoff:3.500A) Processing helix chain 'i' and resid 148 through 165 removed outlier: 3.691A pdb=" N ILE i 152 " --> pdb=" O LYS i 148 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 77 removed outlier: 3.578A pdb=" N TYR j 68 " --> pdb=" O GLU j 64 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 97 removed outlier: 3.997A pdb=" N GLN j 88 " --> pdb=" O GLU j 84 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG j 97 " --> pdb=" O SER j 93 " (cutoff:3.500A) Processing helix chain 'j' and resid 142 through 152 removed outlier: 3.569A pdb=" N GLY j 147 " --> pdb=" O ASP j 143 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER j 151 " --> pdb=" O GLY j 147 " (cutoff:3.500A) Processing helix chain 'j' and resid 159 through 175 removed outlier: 4.122A pdb=" N GLU j 164 " --> pdb=" O GLU j 160 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER j 167 " --> pdb=" O PHE j 163 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA j 173 " --> pdb=" O ALA j 169 " (cutoff:3.500A) Processing helix chain 'k' and resid 52 through 71 removed outlier: 3.791A pdb=" N ILE k 60 " --> pdb=" O PHE k 56 " (cutoff:3.500A) Processing helix chain 'k' and resid 77 through 93 removed outlier: 3.619A pdb=" N SER k 82 " --> pdb=" O GLN k 78 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE k 92 " --> pdb=" O LEU k 88 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG k 93 " --> pdb=" O ALA k 89 " (cutoff:3.500A) Processing helix chain 'k' and resid 136 through 147 removed outlier: 3.630A pdb=" N PHE k 141 " --> pdb=" O GLY k 137 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N SER k 142 " --> pdb=" O PHE k 138 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU k 143 " --> pdb=" O TYR k 139 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS k 146 " --> pdb=" O SER k 142 " (cutoff:3.500A) Processing helix chain 'k' and resid 154 through 171 removed outlier: 3.662A pdb=" N ASP k 159 " --> pdb=" O GLU k 155 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU k 163 " --> pdb=" O ASP k 159 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS k 170 " --> pdb=" O GLN k 166 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG k 171 " --> pdb=" O GLU k 167 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 69 removed outlier: 3.670A pdb=" N THR l 57 " --> pdb=" O GLN l 53 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY l 60 " --> pdb=" O GLU l 56 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU l 68 " --> pdb=" O ARG l 64 " (cutoff:3.500A) Processing helix chain 'l' and resid 76 through 89 Processing helix chain 'l' and resid 133 through 141 removed outlier: 3.519A pdb=" N GLY l 138 " --> pdb=" O THR l 134 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL l 139 " --> pdb=" O PHE l 135 " (cutoff:3.500A) Processing helix chain 'l' and resid 150 through 167 removed outlier: 3.545A pdb=" N LYS l 158 " --> pdb=" O LEU l 154 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA l 164 " --> pdb=" O SER l 160 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG l 167 " --> pdb=" O ALA l 163 " (cutoff:3.500A) Processing helix chain 'l' and resid 193 through 203 removed outlier: 4.345A pdb=" N TRP l 198 " --> pdb=" O GLY l 194 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU l 202 " --> pdb=" O TRP l 198 " (cutoff:3.500A) Processing helix chain 'm' and resid 58 through 78 removed outlier: 3.690A pdb=" N ARG m 67 " --> pdb=" O ALA m 63 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP m 78 " --> pdb=" O TRP m 74 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 100 removed outlier: 3.549A pdb=" N ARG m 91 " --> pdb=" O ASN m 87 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS m 100 " --> pdb=" O LEU m 96 " (cutoff:3.500A) Processing helix chain 'm' and resid 141 through 154 removed outlier: 4.275A pdb=" N SER m 144 " --> pdb=" O ALA m 141 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N MET m 147 " --> pdb=" O SER m 144 " (cutoff:3.500A) Proline residue: m 148 - end of helix removed outlier: 3.776A pdb=" N ASP m 151 " --> pdb=" O PRO m 148 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL m 154 " --> pdb=" O ASP m 151 " (cutoff:3.500A) Processing helix chain 'm' and resid 177 through 194 removed outlier: 3.532A pdb=" N ILE m 181 " --> pdb=" O VAL m 177 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS m 182 " --> pdb=" O GLU m 178 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU m 193 " --> pdb=" O THR m 189 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG m 194 " --> pdb=" O SER m 190 " (cutoff:3.500A) Processing helix chain 'n' and resid 57 through 75 removed outlier: 3.617A pdb=" N HIS n 62 " --> pdb=" O SER n 58 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU n 66 " --> pdb=" O HIS n 62 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL n 71 " --> pdb=" O LEU n 67 " (cutoff:3.500A) Processing helix chain 'n' and resid 79 through 83 Processing helix chain 'n' and resid 89 through 106 removed outlier: 3.602A pdb=" N GLU n 94 " --> pdb=" O SER n 90 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS n 106 " --> pdb=" O GLN n 102 " (cutoff:3.500A) Processing helix chain 'n' and resid 145 through 148 Processing helix chain 'n' and resid 151 through 158 removed outlier: 3.858A pdb=" N LYS n 157 " --> pdb=" O PRO n 153 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL n 158 " --> pdb=" O LEU n 154 " (cutoff:3.500A) Processing helix chain 'n' and resid 162 through 164 No H-bonds generated for 'chain 'n' and resid 162 through 164' Processing helix chain 'n' and resid 170 through 187 Processing helix chain 'n' and resid 220 through 223 removed outlier: 4.232A pdb=" N LYS n 223 " --> pdb=" O ASP n 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 220 through 223' Processing helix chain 'A' and resid 17 through 26 removed outlier: 3.648A pdb=" N PHE A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 25 " --> pdb=" O TYR A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 99 removed outlier: 3.513A pdb=" N ARG A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 120 Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.596A pdb=" N ASN A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.569A pdb=" N GLU A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 240 removed outlier: 3.724A pdb=" N GLU A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 79 through 95 removed outlier: 3.703A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 101 No H-bonds generated for 'chain 'B' and resid 98 through 101' Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.600A pdb=" N ILE B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.813A pdb=" N THR B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 199 removed outlier: 3.550A pdb=" N HIS B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.601A pdb=" N ARG B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 5 Processing helix chain 'C' and resid 19 through 29 Processing helix chain 'C' and resid 80 through 101 removed outlier: 3.582A pdb=" N GLU C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 97 " --> pdb=" O HIS C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.573A pdb=" N LEU C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.677A pdb=" N MET C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 removed outlier: 3.526A pdb=" N GLU C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'D' and resid 16 through 26 removed outlier: 3.628A pdb=" N LYS D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 97 removed outlier: 3.931A pdb=" N ARG D 81 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 removed outlier: 4.039A pdb=" N THR D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 removed outlier: 3.571A pdb=" N LYS D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 199 removed outlier: 4.321A pdb=" N GLU D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 239 Processing helix chain 'E' and resid 14 through 25 removed outlier: 3.696A pdb=" N LEU E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU E 21 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA E 22 " --> pdb=" O TYR E 18 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 95 removed outlier: 4.085A pdb=" N ILE E 81 " --> pdb=" O ARG E 78 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU E 82 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA E 84 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG E 85 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA E 88 " --> pdb=" O ARG E 85 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR E 94 " --> pdb=" O HIS E 91 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR E 95 " --> pdb=" O ASN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 112 removed outlier: 3.592A pdb=" N GLN E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 178 removed outlier: 3.504A pdb=" N ALA E 173 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU E 174 " --> pdb=" O GLY E 170 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 198 removed outlier: 3.524A pdb=" N GLU E 189 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU E 190 " --> pdb=" O LYS E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 240 removed outlier: 3.508A pdb=" N GLU E 230 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU E 237 " --> pdb=" O LYS E 233 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 26 Processing helix chain 'F' and resid 77 through 97 removed outlier: 3.771A pdb=" N ASN F 85 " --> pdb=" O ARG F 81 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER F 94 " --> pdb=" O GLN F 90 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL F 97 " --> pdb=" O TYR F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.601A pdb=" N HIS F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASN F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR F 119 " --> pdb=" O ALA F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 180 removed outlier: 3.813A pdb=" N THR F 169 " --> pdb=" O GLY F 166 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU F 171 " --> pdb=" O LYS F 168 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG F 173 " --> pdb=" O TYR F 170 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR F 174 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU F 175 " --> pdb=" O GLU F 172 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP F 176 " --> pdb=" O ARG F 173 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE F 178 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE F 179 " --> pdb=" O ASP F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 198 removed outlier: 3.607A pdb=" N ILE F 189 " --> pdb=" O PRO F 185 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY F 192 " --> pdb=" O LEU F 188 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 29 removed outlier: 3.704A pdb=" N VAL G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS G 25 " --> pdb=" O GLU G 21 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN G 29 " --> pdb=" O LYS G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 99 removed outlier: 3.600A pdb=" N GLU G 90 " --> pdb=" O ASN G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 120 removed outlier: 3.802A pdb=" N HIS G 119 " --> pdb=" O TYR G 115 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR G 120 " --> pdb=" O VAL G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 178 removed outlier: 4.426A pdb=" N GLN G 166 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER G 167 " --> pdb=" O GLY G 164 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA G 168 " --> pdb=" O ARG G 165 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU G 172 " --> pdb=" O LYS G 169 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU G 173 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N HIS G 178 " --> pdb=" O LEU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 199 removed outlier: 3.602A pdb=" N VAL G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS G 190 " --> pdb=" O ARG G 186 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS G 194 " --> pdb=" O LYS G 190 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU G 198 " --> pdb=" O LYS G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 242 removed outlier: 3.618A pdb=" N ASP G 237 " --> pdb=" O GLN G 233 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU G 242 " --> pdb=" O PHE G 238 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 70 removed outlier: 3.517A pdb=" N GLN 1 69 " --> pdb=" O LEU 1 65 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 88 removed outlier: 3.516A pdb=" N PHE 1 82 " --> pdb=" O ALA 1 78 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU 1 88 " --> pdb=" O GLU 1 84 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 141 removed outlier: 3.797A pdb=" N TYR 1 135 " --> pdb=" O THR 1 132 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLY 1 136 " --> pdb=" O PHE 1 133 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS 1 138 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP 1 139 " --> pdb=" O GLY 1 136 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS 1 140 " --> pdb=" O TYR 1 137 " (cutoff:3.500A) Processing helix chain '1' and resid 148 through 165 Processing helix chain '1' and resid 190 through 193 No H-bonds generated for 'chain '1' and resid 190 through 193' Processing helix chain '2' and resid 49 through 70 removed outlier: 3.506A pdb=" N GLU 2 53 " --> pdb=" O ALA 2 49 " (cutoff:3.500A) Processing helix chain '2' and resid 76 through 88 removed outlier: 3.520A pdb=" N GLN 2 85 " --> pdb=" O GLN 2 81 " (cutoff:3.500A) Processing helix chain '2' and resid 131 through 141 removed outlier: 4.128A pdb=" N VAL 2 137 " --> pdb=" O ALA 2 133 " (cutoff:3.500A) Processing helix chain '2' and resid 148 through 165 removed outlier: 3.787A pdb=" N TRP 2 164 " --> pdb=" O GLN 2 160 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 6 removed outlier: 3.633A pdb=" N ILE 3 6 " --> pdb=" O PRO 3 3 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 3 through 6' Processing helix chain '3' and resid 56 through 77 Processing helix chain '3' and resid 83 through 96 Processing helix chain '3' and resid 142 through 152 removed outlier: 3.749A pdb=" N SER 3 151 " --> pdb=" O GLY 3 147 " (cutoff:3.500A) Processing helix chain '3' and resid 159 through 176 removed outlier: 3.992A pdb=" N GLU 3 164 " --> pdb=" O GLU 3 160 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER 3 167 " --> pdb=" O PHE 3 163 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN 3 168 " --> pdb=" O GLU 3 164 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA 3 173 " --> pdb=" O ALA 3 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP 3 175 " --> pdb=" O LEU 3 171 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG 3 176 " --> pdb=" O ASN 3 172 " (cutoff:3.500A) Processing helix chain '4' and resid 52 through 71 removed outlier: 3.501A pdb=" N ILE 4 60 " --> pdb=" O PHE 4 56 " (cutoff:3.500A) Processing helix chain '4' and resid 77 through 93 removed outlier: 3.905A pdb=" N ARG 4 93 " --> pdb=" O ALA 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 136 through 147 removed outlier: 3.524A pdb=" N THR 4 140 " --> pdb=" O SER 4 136 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N SER 4 142 " --> pdb=" O PHE 4 138 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU 4 143 " --> pdb=" O TYR 4 139 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS 4 146 " --> pdb=" O SER 4 142 " (cutoff:3.500A) Processing helix chain '4' and resid 154 through 171 removed outlier: 3.522A pdb=" N ASP 4 159 " --> pdb=" O GLU 4 155 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU 4 163 " --> pdb=" O ASP 4 159 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS 4 170 " --> pdb=" O GLN 4 166 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 69 removed outlier: 3.617A pdb=" N GLU 5 56 " --> pdb=" O CYS 5 52 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR 5 57 " --> pdb=" O GLN 5 53 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU 5 59 " --> pdb=" O TRP 5 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY 5 60 " --> pdb=" O GLU 5 56 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU 5 68 " --> pdb=" O ARG 5 64 " (cutoff:3.500A) Processing helix chain '5' and resid 76 through 89 removed outlier: 3.739A pdb=" N LEU 5 83 " --> pdb=" O ALA 5 79 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN 5 85 " --> pdb=" O LYS 5 81 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN 5 89 " --> pdb=" O ASN 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 131 through 142 removed outlier: 4.505A pdb=" N THR 5 134 " --> pdb=" O SER 5 131 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA 5 136 " --> pdb=" O GLN 5 133 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL 5 139 " --> pdb=" O ALA 5 136 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP 5 141 " --> pdb=" O GLY 5 138 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER 5 142 " --> pdb=" O VAL 5 139 " (cutoff:3.500A) Processing helix chain '5' and resid 150 through 167 removed outlier: 3.910A pdb=" N ARG 5 167 " --> pdb=" O ALA 5 163 " (cutoff:3.500A) Processing helix chain '5' and resid 193 through 204 removed outlier: 4.219A pdb=" N TRP 5 198 " --> pdb=" O GLY 5 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS 5 199 " --> pdb=" O GLU 5 195 " (cutoff:3.500A) Processing helix chain '6' and resid 58 through 79 removed outlier: 3.623A pdb=" N ASP 6 78 " --> pdb=" O TRP 6 74 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 99 removed outlier: 3.815A pdb=" N ARG 6 91 " --> pdb=" O ASN 6 87 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS 6 95 " --> pdb=" O ARG 6 91 " (cutoff:3.500A) Processing helix chain '6' and resid 141 through 153 removed outlier: 4.553A pdb=" N SER 6 144 " --> pdb=" O ALA 6 141 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N MET 6 147 " --> pdb=" O SER 6 144 " (cutoff:3.500A) Proline residue: 6 148 - end of helix removed outlier: 3.514A pdb=" N ASN 6 152 " --> pdb=" O PHE 6 149 " (cutoff:3.500A) Processing helix chain '6' and resid 177 through 194 removed outlier: 3.636A pdb=" N LYS 6 182 " --> pdb=" O GLU 6 178 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU 6 193 " --> pdb=" O THR 6 189 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG 6 194 " --> pdb=" O SER 6 190 " (cutoff:3.500A) Processing helix chain '7' and resid 57 through 75 removed outlier: 3.714A pdb=" N HIS 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU 7 66 " --> pdb=" O HIS 7 62 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR 7 72 " --> pdb=" O LYS 7 68 " (cutoff:3.500A) Processing helix chain '7' and resid 89 through 106 removed outlier: 3.773A pdb=" N LYS 7 106 " --> pdb=" O GLN 7 102 " (cutoff:3.500A) Processing helix chain '7' and resid 147 through 157 removed outlier: 4.720A pdb=" N ASN 7 152 " --> pdb=" O ALA 7 148 " (cutoff:3.500A) Proline residue: 7 153 - end of helix removed outlier: 4.126A pdb=" N LYS 7 157 " --> pdb=" O PRO 7 153 " (cutoff:3.500A) Processing helix chain '7' and resid 162 through 164 No H-bonds generated for 'chain '7' and resid 162 through 164' Processing helix chain '7' and resid 170 through 187 Processing helix chain 'H' and resid 43 through 67 removed outlier: 3.925A pdb=" N LYS H 48 " --> pdb=" O PRO H 44 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA H 67 " --> pdb=" O ILE H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 91 removed outlier: 3.584A pdb=" N ILE H 84 " --> pdb=" O HIS H 80 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP H 87 " --> pdb=" O ASP H 83 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG H 88 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'H' and resid 208 through 210 No H-bonds generated for 'chain 'H' and resid 208 through 210' Processing helix chain 'H' and resid 216 through 222 removed outlier: 3.510A pdb=" N LEU H 221 " --> pdb=" O GLN H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 230 Processing helix chain 'H' and resid 232 through 238 removed outlier: 3.985A pdb=" N THR H 237 " --> pdb=" O GLU H 233 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU H 238 " --> pdb=" O ARG H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 267 removed outlier: 3.565A pdb=" N ALA H 260 " --> pdb=" O LYS H 256 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG H 266 " --> pdb=" O ALA H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 300 removed outlier: 3.666A pdb=" N VAL H 291 " --> pdb=" O GLY H 287 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE H 295 " --> pdb=" O VAL H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 339 removed outlier: 4.172A pdb=" N THR H 332 " --> pdb=" O GLU H 328 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU H 335 " --> pdb=" O ARG H 331 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN H 339 " --> pdb=" O GLU H 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 366 No H-bonds generated for 'chain 'H' and resid 363 through 366' Processing helix chain 'H' and resid 382 through 393 removed outlier: 3.576A pdb=" N HIS H 392 " --> pdb=" O ILE H 388 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 410 Processing helix chain 'H' and resid 416 through 432 removed outlier: 3.620A pdb=" N ARG H 420 " --> pdb=" O GLY H 416 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER H 421 " --> pdb=" O ALA H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 454 Processing helix chain 'H' and resid 459 through 466 removed outlier: 3.912A pdb=" N GLN H 465 " --> pdb=" O SER H 461 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR H 466 " --> pdb=" O ARG H 462 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 76 removed outlier: 3.525A pdb=" N MET I 62 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS I 68 " --> pdb=" O ARG I 64 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU I 69 " --> pdb=" O ILE I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 100 removed outlier: 3.726A pdb=" N GLU I 91 " --> pdb=" O LYS I 87 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS I 93 " --> pdb=" O GLN I 89 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS I 94 " --> pdb=" O GLU I 90 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG I 100 " --> pdb=" O LEU I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 171 removed outlier: 4.101A pdb=" N MET I 171 " --> pdb=" O MET I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 194 removed outlier: 3.567A pdb=" N ILE I 194 " --> pdb=" O GLN I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 203 No H-bonds generated for 'chain 'I' and resid 200 through 203' Processing helix chain 'I' and resid 205 through 211 removed outlier: 3.607A pdb=" N GLU I 209 " --> pdb=" O PRO I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 240 removed outlier: 3.502A pdb=" N ALA I 233 " --> pdb=" O LYS I 229 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR I 240 " --> pdb=" O VAL I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 252 Processing helix chain 'I' and resid 259 through 274 removed outlier: 3.975A pdb=" N PHE I 268 " --> pdb=" O CYS I 264 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS I 269 " --> pdb=" O ARG I 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 289 removed outlier: 3.779A pdb=" N ILE I 287 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR I 289 " --> pdb=" O ALA I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 313 removed outlier: 3.615A pdb=" N ILE I 302 " --> pdb=" O GLY I 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 339 No H-bonds generated for 'chain 'I' and resid 336 through 339' Processing helix chain 'I' and resid 357 through 367 removed outlier: 3.511A pdb=" N HIS I 365 " --> pdb=" O ILE I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 383 removed outlier: 3.709A pdb=" N VAL I 381 " --> pdb=" O LEU I 377 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR I 382 " --> pdb=" O GLU I 378 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR I 383 " --> pdb=" O THR I 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 377 through 383' Processing helix chain 'I' and resid 389 through 406 Processing helix chain 'I' and resid 413 through 426 removed outlier: 3.534A pdb=" N LYS I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 436 No H-bonds generated for 'chain 'I' and resid 433 through 436' Processing helix chain 'K' and resid 41 through 89 removed outlier: 3.615A pdb=" N SER K 45 " --> pdb=" O SER K 41 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP K 46 " --> pdb=" O ASN K 42 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE K 49 " --> pdb=" O SER K 45 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS K 52 " --> pdb=" O TYR K 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS K 53 " --> pdb=" O PHE K 49 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU K 57 " --> pdb=" O LYS K 53 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR K 58 " --> pdb=" O LEU K 54 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU K 60 " --> pdb=" O LYS K 56 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU K 61 " --> pdb=" O GLU K 57 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR K 62 " --> pdb=" O TYR K 58 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU K 65 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP K 66 " --> pdb=" O THR K 62 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE K 68 " --> pdb=" O GLN K 64 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS K 69 " --> pdb=" O GLU K 65 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP K 70 " --> pdb=" O ASP K 66 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN K 72 " --> pdb=" O ILE K 68 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG K 73 " --> pdb=" O LYS K 69 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG K 77 " --> pdb=" O ARG K 73 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS K 80 " --> pdb=" O LYS K 76 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU K 85 " --> pdb=" O ARG K 81 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL K 86 " --> pdb=" O ALA K 82 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS K 87 " --> pdb=" O GLN K 83 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 193 removed outlier: 4.685A pdb=" N LEU K 190 " --> pdb=" O GLU K 186 " (cutoff:3.500A) Proline residue: K 191 - end of helix Processing helix chain 'K' and resid 196 through 201 Processing helix chain 'K' and resid 219 through 229 removed outlier: 3.511A pdb=" N VAL K 226 " --> pdb=" O LEU K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 263 Processing helix chain 'K' and resid 287 through 305 removed outlier: 3.957A pdb=" N ARG K 294 " --> pdb=" O ARG K 290 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE K 295 " --> pdb=" O GLU K 291 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP K 304 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY K 305 " --> pdb=" O THR K 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 359 removed outlier: 3.622A pdb=" N ILE K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR K 355 " --> pdb=" O LEU K 351 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS K 359 " --> pdb=" O THR K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 372 No H-bonds generated for 'chain 'K' and resid 369 through 372' Processing helix chain 'K' and resid 380 through 397 removed outlier: 3.996A pdb=" N VAL K 395 " --> pdb=" O GLY K 391 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG K 396 " --> pdb=" O LEU K 392 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 412 Processing helix chain 'L' and resid 53 through 99 removed outlier: 3.750A pdb=" N GLN L 59 " --> pdb=" O LYS L 55 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE L 60 " --> pdb=" O ALA L 56 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS L 63 " --> pdb=" O GLN L 59 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP L 72 " --> pdb=" O ARG L 68 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN L 76 " --> pdb=" O ASP L 72 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN L 79 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN L 80 " --> pdb=" O GLN L 76 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE L 81 " --> pdb=" O ARG L 77 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU L 84 " --> pdb=" O ASN L 80 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS L 86 " --> pdb=" O ARG L 82 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP L 89 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS L 90 " --> pdb=" O LYS L 86 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE L 95 " --> pdb=" O THR L 91 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN L 99 " --> pdb=" O ILE L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 172 removed outlier: 3.591A pdb=" N THR L 171 " --> pdb=" O VAL L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 194 removed outlier: 3.744A pdb=" N ARG L 191 " --> pdb=" O THR L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 202 No H-bonds generated for 'chain 'L' and resid 199 through 202' Processing helix chain 'L' and resid 204 through 210 removed outlier: 3.749A pdb=" N VAL L 210 " --> pdb=" O ILE L 206 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 238 removed outlier: 3.673A pdb=" N ALA L 232 " --> pdb=" O LYS L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 251 removed outlier: 3.938A pdb=" N ILE L 251 " --> pdb=" O ALA L 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 248 through 251' Processing helix chain 'L' and resid 258 through 272 removed outlier: 3.878A pdb=" N ILE L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG L 264 " --> pdb=" O ALA L 260 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE L 267 " --> pdb=" O ILE L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 312 removed outlier: 3.526A pdb=" N ILE L 301 " --> pdb=" O ALA L 297 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG L 303 " --> pdb=" O ARG L 299 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR L 310 " --> pdb=" O MET L 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 332 No H-bonds generated for 'chain 'L' and resid 330 through 332' Processing helix chain 'L' and resid 335 through 338 No H-bonds generated for 'chain 'L' and resid 335 through 338' Processing helix chain 'L' and resid 356 through 366 removed outlier: 3.609A pdb=" N LYS L 362 " --> pdb=" O LEU L 358 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS L 364 " --> pdb=" O ILE L 360 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA L 366 " --> pdb=" O LYS L 362 " (cutoff:3.500A) Processing helix chain 'L' and resid 375 through 382 removed outlier: 3.720A pdb=" N ALA L 379 " --> pdb=" O PHE L 376 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL L 380 " --> pdb=" O GLU L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 388 through 404 removed outlier: 3.623A pdb=" N THR L 396 " --> pdb=" O ARG L 392 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 429 removed outlier: 3.625A pdb=" N ARG L 420 " --> pdb=" O MET L 416 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL L 425 " --> pdb=" O LYS L 421 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU L 428 " --> pdb=" O GLU L 424 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 72 removed outlier: 3.547A pdb=" N LEU M 36 " --> pdb=" O THR M 32 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN M 39 " --> pdb=" O LYS M 35 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE M 41 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ARG M 42 " --> pdb=" O ASP M 38 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE M 43 " --> pdb=" O ASN M 39 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU M 59 " --> pdb=" O ASN M 55 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU M 60 " --> pdb=" O ASN M 56 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE M 62 " --> pdb=" O MET M 58 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS M 66 " --> pdb=" O ILE M 62 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU M 67 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS M 68 " --> pdb=" O ASP M 64 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN M 71 " --> pdb=" O GLU M 67 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN M 72 " --> pdb=" O LYS M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 170 Processing helix chain 'M' and resid 180 through 182 No H-bonds generated for 'chain 'M' and resid 180 through 182' Processing helix chain 'M' and resid 187 through 196 Processing helix chain 'M' and resid 198 through 202 Processing helix chain 'M' and resid 204 through 210 Processing helix chain 'M' and resid 228 through 239 Processing helix chain 'M' and resid 248 through 251 No H-bonds generated for 'chain 'M' and resid 248 through 251' Processing helix chain 'M' and resid 258 through 272 removed outlier: 3.589A pdb=" N LEU M 262 " --> pdb=" O GLU M 258 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL M 263 " --> pdb=" O GLY M 259 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU M 272 " --> pdb=" O ALA M 268 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 312 removed outlier: 3.622A pdb=" N ASN M 310 " --> pdb=" O LEU M 306 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN M 311 " --> pdb=" O GLU M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 354 through 365 removed outlier: 4.081A pdb=" N ALA M 358 " --> pdb=" O GLU M 354 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN M 359 " --> pdb=" O ASP M 355 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS M 364 " --> pdb=" O ILE M 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 376 through 382 removed outlier: 3.541A pdb=" N ARG M 381 " --> pdb=" O GLN M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 405 Processing helix chain 'M' and resid 412 through 422 removed outlier: 3.744A pdb=" N SER M 420 " --> pdb=" O VAL M 416 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU M 421 " --> pdb=" O GLU M 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 64 removed outlier: 4.167A pdb=" N LYS J 20 " --> pdb=" O GLU J 16 " (cutoff:3.500A) Proline residue: J 21 - end of helix removed outlier: 4.227A pdb=" N LYS J 26 " --> pdb=" O TYR J 22 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE J 27 " --> pdb=" O PHE J 23 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR J 30 " --> pdb=" O LYS J 26 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS J 33 " --> pdb=" O GLU J 29 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU J 39 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN J 40 " --> pdb=" O SER J 36 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG J 42 " --> pdb=" O THR J 38 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG J 43 " --> pdb=" O GLU J 39 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA J 50 " --> pdb=" O ALA J 46 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL J 55 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP J 60 " --> pdb=" O ARG J 56 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU J 62 " --> pdb=" O ILE J 58 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ARG J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 140 removed outlier: 3.559A pdb=" N LEU J 136 " --> pdb=" O PRO J 132 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET J 137 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU J 140 " --> pdb=" O LEU J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 150 No H-bonds generated for 'chain 'J' and resid 147 through 150' Processing helix chain 'J' and resid 154 through 163 removed outlier: 4.093A pdb=" N LYS J 158 " --> pdb=" O THR J 154 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU J 159 " --> pdb=" O LYS J 155 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU J 162 " --> pdb=" O LYS J 158 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL J 163 " --> pdb=" O GLU J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 169 Processing helix chain 'J' and resid 171 through 177 removed outlier: 3.500A pdb=" N GLU J 175 " --> pdb=" O PRO J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 206 removed outlier: 3.610A pdb=" N ALA J 199 " --> pdb=" O LYS J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 231 through 239 removed outlier: 3.774A pdb=" N MET J 236 " --> pdb=" O GLU J 232 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU J 239 " --> pdb=" O VAL J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 258 No H-bonds generated for 'chain 'J' and resid 255 through 258' Processing helix chain 'J' and resid 266 through 277 removed outlier: 3.544A pdb=" N LEU J 276 " --> pdb=" O MET J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 304 No H-bonds generated for 'chain 'J' and resid 302 through 304' Processing helix chain 'J' and resid 321 through 334 removed outlier: 3.688A pdb=" N ALA J 325 " --> pdb=" O VAL J 321 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU J 326 " --> pdb=" O ALA J 322 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS J 331 " --> pdb=" O ILE J 327 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS J 334 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 349 removed outlier: 3.531A pdb=" N ALA J 347 " --> pdb=" O LEU J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 355 through 371 removed outlier: 3.760A pdb=" N CYS J 362 " --> pdb=" O VAL J 358 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 397 removed outlier: 3.721A pdb=" N GLU J 383 " --> pdb=" O GLN J 379 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY J 387 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR J 396 " --> pdb=" O LYS J 392 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'a' and resid 159 through 162 Processing sheet with id= B, first strand: chain 'a' and resid 63 through 65 removed outlier: 3.568A pdb=" N LYS a 147 " --> pdb=" O VAL a 155 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL a 155 " --> pdb=" O LYS a 147 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'b' and resid 161 through 164 Processing sheet with id= D, first strand: chain 'b' and resid 156 through 158 removed outlier: 3.546A pdb=" N ASP b 140 " --> pdb=" O GLY b 144 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE b 71 " --> pdb=" O THR b 68 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA b 73 " --> pdb=" O LEU b 66 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU b 66 " --> pdb=" O ALA b 73 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N TYR b 75 " --> pdb=" O VAL b 64 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL b 64 " --> pdb=" O TYR b 75 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'c' and resid 161 through 164 removed outlier: 3.879A pdb=" N GLY c 42 " --> pdb=" O ALA c 39 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'c' and resid 65 through 67 removed outlier: 3.645A pdb=" N PHE c 134 " --> pdb=" O SER c 150 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP c 140 " --> pdb=" O GLY c 144 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'd' and resid 159 through 162 removed outlier: 3.517A pdb=" N ASP d 218 " --> pdb=" O LYS d 214 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'd' and resid 62 through 64 Processing sheet with id= I, first strand: chain 'e' and resid 161 through 164 Processing sheet with id= J, first strand: chain 'e' and resid 69 through 72 removed outlier: 3.581A pdb=" N GLY e 138 " --> pdb=" O GLN e 146 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY e 144 " --> pdb=" O ASP e 140 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR e 157 " --> pdb=" O HIS e 149 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'f' and resid 157 through 160 removed outlier: 3.608A pdb=" N THR f 222 " --> pdb=" O ILE f 214 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'f' and resid 62 through 64 removed outlier: 3.563A pdb=" N LEU f 131 " --> pdb=" O PHE f 146 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY f 135 " --> pdb=" O HIS f 142 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'g' and resid 158 through 161 removed outlier: 3.696A pdb=" N GLU g 211 " --> pdb=" O VAL g 46 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'g' and resid 63 through 66 removed outlier: 3.619A pdb=" N MET g 146 " --> pdb=" O TRP g 154 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP g 154 " --> pdb=" O MET g 146 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'h' and resid 124 through 128 Processing sheet with id= P, first strand: chain 'h' and resid 34 through 36 removed outlier: 4.174A pdb=" N VAL h 110 " --> pdb=" O LEU h 122 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'h' and resid 20 through 22 removed outlier: 3.747A pdb=" N ASN h 28 " --> pdb=" O THR h 20 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR h 22 " --> pdb=" O ILE h 26 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE h 26 " --> pdb=" O THR h 22 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'i' and resid 124 through 128 removed outlier: 6.033A pdb=" N THR i 2 " --> pdb=" O ASP i 17 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP i 17 " --> pdb=" O THR i 2 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL i 175 " --> pdb=" O LEU i 187 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'i' and resid 119 through 121 removed outlier: 3.702A pdb=" N ASP i 104 " --> pdb=" O GLY i 107 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY i 102 " --> pdb=" O HIS i 109 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N CYS i 43 " --> pdb=" O ARG i 36 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ARG i 36 " --> pdb=" O CYS i 43 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLY i 45 " --> pdb=" O LEU i 34 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU i 34 " --> pdb=" O GLY i 45 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'j' and resid 135 through 139 removed outlier: 5.517A pdb=" N ILE j 10 " --> pdb=" O ASP j 25 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP j 25 " --> pdb=" O ILE j 10 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA j 184 " --> pdb=" O LEU j 199 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'j' and resid 42 through 45 Processing sheet with id= V, first strand: chain 'j' and resid 28 through 30 removed outlier: 6.436A pdb=" N SER j 30 " --> pdb=" O GLY j 34 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLY j 34 " --> pdb=" O SER j 30 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'k' and resid 130 through 132 removed outlier: 4.540A pdb=" N VAL k 181 " --> pdb=" O VAL k 192 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'k' and resid 125 through 127 removed outlier: 6.564A pdb=" N MET k 44 " --> pdb=" O GLN k 37 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLN k 37 " --> pdb=" O MET k 44 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N PHE k 46 " --> pdb=" O THR k 35 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N THR k 35 " --> pdb=" O PHE k 46 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'l' and resid 126 through 130 Processing sheet with id= Z, first strand: chain 'l' and resid 41 through 43 removed outlier: 3.584A pdb=" N THR l 105 " --> pdb=" O GLY l 109 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'l' and resid 178 through 181 Processing sheet with id= AB, first strand: chain 'l' and resid 20 through 22 removed outlier: 3.540A pdb=" N SER l 28 " --> pdb=" O ALA l 20 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA l 22 " --> pdb=" O VAL l 26 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL l 26 " --> pdb=" O ALA l 22 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'm' and resid 136 through 140 removed outlier: 5.097A pdb=" N THR m 11 " --> pdb=" O ASP m 26 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'm' and resid 50 through 56 removed outlier: 3.711A pdb=" N ASN m 55 " --> pdb=" O HIS m 108 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR m 109 " --> pdb=" O PHE m 125 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'm' and resid 29 through 31 removed outlier: 6.603A pdb=" N THR m 31 " --> pdb=" O ILE m 35 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE m 35 " --> pdb=" O THR m 31 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'n' and resid 141 through 143 Processing sheet with id= AG, first strand: chain 'n' and resid 42 through 44 Processing sheet with id= AH, first strand: chain 'A' and resid 159 through 162 Processing sheet with id= AI, first strand: chain 'A' and resid 63 through 65 Processing sheet with id= AJ, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= AK, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.469A pdb=" N ALA B 73 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU B 66 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TYR B 75 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 64 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.559A pdb=" N ARG C 216 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 65 through 67 Processing sheet with id= AN, first strand: chain 'D' and resid 159 through 162 removed outlier: 3.610A pdb=" N ASP D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'D' and resid 69 through 75 removed outlier: 3.518A pdb=" N THR D 131 " --> pdb=" O THR D 148 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'E' and resid 161 through 164 removed outlier: 3.581A pdb=" N VAL E 38 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'E' and resid 156 through 158 removed outlier: 6.417A pdb=" N CYS E 68 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU E 61 " --> pdb=" O CYS E 68 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N MET E 70 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE E 59 " --> pdb=" O MET E 70 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'F' and resid 157 through 160 removed outlier: 3.704A pdb=" N ILE F 212 " --> pdb=" O TYR F 224 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'F' and resid 62 through 64 removed outlier: 3.856A pdb=" N GLY F 140 " --> pdb=" O ASP F 137 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'G' and resid 158 through 161 Processing sheet with id= AU, first strand: chain 'G' and resid 63 through 66 removed outlier: 3.591A pdb=" N MET G 146 " --> pdb=" O TRP G 154 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP G 154 " --> pdb=" O MET G 146 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain '1' and resid 124 through 128 Processing sheet with id= AW, first strand: chain '1' and resid 34 through 36 Processing sheet with id= AX, first strand: chain '1' and resid 20 through 22 removed outlier: 3.658A pdb=" N ASN 1 28 " --> pdb=" O THR 1 20 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR 1 22 " --> pdb=" O ILE 1 26 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE 1 26 " --> pdb=" O THR 1 22 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain '2' and resid 124 through 127 Processing sheet with id= AZ, first strand: chain '2' and resid 119 through 121 removed outlier: 3.669A pdb=" N TYR 2 97 " --> pdb=" O ALA 2 46 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N CYS 2 43 " --> pdb=" O ARG 2 36 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ARG 2 36 " --> pdb=" O CYS 2 43 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLY 2 45 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU 2 34 " --> pdb=" O GLY 2 45 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain '2' and resid 20 through 22 removed outlier: 5.805A pdb=" N GLN 2 22 " --> pdb=" O VAL 2 26 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL 2 26 " --> pdb=" O GLN 2 22 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain '3' and resid 135 through 139 removed outlier: 3.539A pdb=" N VAL 3 11 " --> pdb=" O SER 3 138 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE 3 10 " --> pdb=" O ASP 3 25 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP 3 25 " --> pdb=" O ILE 3 10 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA 3 184 " --> pdb=" O LEU 3 199 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain '3' and resid 42 through 45 removed outlier: 4.638A pdb=" N ILE 3 120 " --> pdb=" O ALA 3 132 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA 3 132 " --> pdb=" O ILE 3 120 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain '3' and resid 28 through 30 removed outlier: 3.581A pdb=" N SER 3 36 " --> pdb=" O LEU 3 28 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER 3 30 " --> pdb=" O GLY 3 34 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLY 3 34 " --> pdb=" O SER 3 30 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain '4' and resid 130 through 132 removed outlier: 4.435A pdb=" N VAL 4 181 " --> pdb=" O VAL 4 192 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain '4' and resid 124 through 127 removed outlier: 3.839A pdb=" N THR 4 124 " --> pdb=" O ASP 4 120 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP 4 120 " --> pdb=" O THR 4 124 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N MET 4 44 " --> pdb=" O GLN 4 37 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLN 4 37 " --> pdb=" O MET 4 44 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE 4 46 " --> pdb=" O THR 4 35 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR 4 35 " --> pdb=" O PHE 4 46 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain '4' and resid 21 through 23 removed outlier: 3.865A pdb=" N LYS 4 29 " --> pdb=" O VAL 4 21 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ARG 4 23 " --> pdb=" O VAL 4 27 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL 4 27 " --> pdb=" O ARG 4 23 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain '5' and resid 126 through 130 removed outlier: 3.504A pdb=" N ALA 5 5 " --> pdb=" O PHE 5 127 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain '5' and resid 34 through 36 removed outlier: 4.345A pdb=" N MET 5 100 " --> pdb=" O THR 5 44 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR 5 105 " --> pdb=" O GLY 5 109 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE 5 112 " --> pdb=" O GLY 5 124 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY 5 124 " --> pdb=" O ILE 5 112 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain '5' and resid 178 through 181 Processing sheet with id= BK, first strand: chain '6' and resid 136 through 140 removed outlier: 5.085A pdb=" N THR 6 11 " --> pdb=" O ASP 6 26 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY 6 211 " --> pdb=" O THR 6 208 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain '6' and resid 50 through 56 removed outlier: 4.028A pdb=" N THR 6 109 " --> pdb=" O PHE 6 125 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL 6 122 " --> pdb=" O GLU 6 134 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain '6' and resid 29 through 31 removed outlier: 6.567A pdb=" N THR 6 31 " --> pdb=" O ILE 6 35 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE 6 35 " --> pdb=" O THR 6 31 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain '7' and resid 141 through 143 removed outlier: 3.611A pdb=" N LEU 7 142 " --> pdb=" O SER 7 13 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain '7' and resid 42 through 44 Processing sheet with id= BP, first strand: chain 'H' and resid 154 through 157 removed outlier: 3.548A pdb=" N TYR H 145 " --> pdb=" O VAL H 157 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS H 104 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN H 148 " --> pdb=" O CYS H 102 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N CYS H 102 " --> pdb=" O ASN H 148 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU H 185 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP H 177 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE H 183 " --> pdb=" O ASP H 177 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'H' and resid 373 through 376 removed outlier: 3.774A pdb=" N TYR H 249 " --> pdb=" O VAL H 375 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ILE H 246 " --> pdb=" O ILE H 349 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL H 351 " --> pdb=" O ILE H 246 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU H 248 " --> pdb=" O VAL H 351 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE H 353 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS H 304 " --> pdb=" O LYS H 350 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N MET H 352 " --> pdb=" O CYS H 304 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE H 306 " --> pdb=" O MET H 352 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ALA H 354 " --> pdb=" O ILE H 306 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N PHE H 308 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR H 270 " --> pdb=" O ILE H 305 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE H 307 " --> pdb=" O THR H 270 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE H 272 " --> pdb=" O PHE H 307 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ASP H 309 " --> pdb=" O ILE H 272 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL H 274 " --> pdb=" O ASP H 309 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'I' and resid 146 through 149 removed outlier: 3.517A pdb=" N VAL I 147 " --> pdb=" O GLY I 107 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE I 119 " --> pdb=" O GLU I 110 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE I 112 " --> pdb=" O HIS I 117 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N HIS I 117 " --> pdb=" O ILE I 112 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'I' and resid 346 through 349 removed outlier: 3.585A pdb=" N ILE I 220 " --> pdb=" O ARG I 346 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR I 222 " --> pdb=" O ILE I 348 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER I 277 " --> pdb=" O LYS I 323 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE I 325 " --> pdb=" O SER I 277 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL I 279 " --> pdb=" O ILE I 325 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALA I 327 " --> pdb=" O VAL I 279 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE I 281 " --> pdb=" O ALA I 327 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR I 243 " --> pdb=" O ILE I 278 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE I 280 " --> pdb=" O THR I 243 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU I 245 " --> pdb=" O PHE I 280 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP I 282 " --> pdb=" O LEU I 245 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE I 247 " --> pdb=" O ASP I 282 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'K' and resid 117 through 121 removed outlier: 6.549A pdb=" N SER K 111 " --> pdb=" O PHE K 99 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N PHE K 99 " --> pdb=" O SER K 111 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET K 135 " --> pdb=" O PHE K 99 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP K 148 " --> pdb=" O ALA K 138 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'K' and resid 315 through 317 removed outlier: 6.436A pdb=" N VAL K 209 " --> pdb=" O MET K 316 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU K 210 " --> pdb=" O ASP K 335 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LYS K 337 " --> pdb=" O LEU K 210 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR K 212 " --> pdb=" O LYS K 337 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU K 339 " --> pdb=" O TYR K 212 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'K' and resid 233 through 237 Processing sheet with id= BW, first strand: chain 'L' and resid 126 through 129 removed outlier: 3.542A pdb=" N LYS L 110 " --> pdb=" O ILE L 118 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LYS L 120 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL L 108 " --> pdb=" O LYS L 120 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG L 145 " --> pdb=" O LEU L 159 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG L 157 " --> pdb=" O THR L 147 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP L 149 " --> pdb=" O ILE L 155 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE L 155 " --> pdb=" O ASP L 149 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'L' and resid 345 through 349 removed outlier: 3.526A pdb=" N TYR L 221 " --> pdb=" O VAL L 347 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY L 222 " --> pdb=" O THR L 327 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS L 276 " --> pdb=" O LYS L 322 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE L 324 " --> pdb=" O CYS L 276 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE L 278 " --> pdb=" O ILE L 324 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ALA L 326 " --> pdb=" O ILE L 278 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET L 280 " --> pdb=" O ALA L 326 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN L 242 " --> pdb=" O ILE L 277 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE L 279 " --> pdb=" O ASN L 242 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE L 244 " --> pdb=" O PHE L 279 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASP L 281 " --> pdb=" O ILE L 244 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER L 246 " --> pdb=" O ASP L 281 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'M' and resid 145 through 147 removed outlier: 7.259A pdb=" N VAL M 118 " --> pdb=" O VAL M 83 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL M 85 " --> pdb=" O ALA M 116 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA M 116 " --> pdb=" O VAL M 85 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'M' and resid 345 through 349 removed outlier: 3.578A pdb=" N ARG M 345 " --> pdb=" O GLY M 217 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ALA M 218 " --> pdb=" O VAL M 321 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL M 323 " --> pdb=" O ALA M 218 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N MET M 220 " --> pdb=" O VAL M 323 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA M 325 " --> pdb=" O MET M 220 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N GLY M 222 " --> pdb=" O ALA M 325 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR M 327 " --> pdb=" O GLY M 222 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR M 276 " --> pdb=" O LYS M 322 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU M 324 " --> pdb=" O THR M 276 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE M 278 " --> pdb=" O LEU M 324 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ALA M 326 " --> pdb=" O ILE M 278 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE M 280 " --> pdb=" O ALA M 326 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR M 242 " --> pdb=" O ILE M 277 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N PHE M 279 " --> pdb=" O THR M 242 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU M 244 " --> pdb=" O PHE M 279 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASP M 281 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU M 246 " --> pdb=" O ASP M 281 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'J' and resid 71 through 74 Processing sheet with id= CB, first strand: chain 'J' and resid 93 through 97 removed outlier: 3.688A pdb=" N LYS J 77 " --> pdb=" O LEU J 85 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS J 87 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL J 75 " --> pdb=" O LYS J 87 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'J' and resid 209 through 212 removed outlier: 3.778A pdb=" N GLY J 189 " --> pdb=" O THR J 294 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE J 186 " --> pdb=" O ASP J 311 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS J 313 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N TYR J 188 " --> pdb=" O LYS J 313 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU J 315 " --> pdb=" O TYR J 188 " (cutoff:3.500A) 2821 hydrogen bonds defined for protein. 8004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 27.55 Time building geometry restraints manager: 22.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.17: 51 1.17 - 1.35: 21732 1.35 - 1.52: 33818 1.52 - 1.70: 13040 1.70 - 1.87: 403 Bond restraints: 69044 Sorted by residual: bond pdb=" C GLU 2 226 " pdb=" O GLU 2 226 " ideal model delta sigma weight residual 1.231 0.999 0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C THR C 244 " pdb=" O THR C 244 " ideal model delta sigma weight residual 1.231 0.999 0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C ASN g 244 " pdb=" O ASN g 244 " ideal model delta sigma weight residual 1.231 0.999 0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C LEU I 437 " pdb=" OXT LEU I 437 " ideal model delta sigma weight residual 1.231 0.999 0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C ALA M 434 " pdb=" OXT ALA M 434 " ideal model delta sigma weight residual 1.231 0.999 0.232 2.00e-02 2.50e+03 1.34e+02 ... (remaining 69039 not shown) Histogram of bond angle deviations from ideal: 93.87 - 103.51: 700 103.51 - 113.16: 38214 113.16 - 122.80: 46994 122.80 - 132.44: 7331 132.44 - 142.08: 79 Bond angle restraints: 93318 Sorted by residual: angle pdb=" PB ATP H 501 " pdb=" O3B ATP H 501 " pdb=" PG ATP H 501 " ideal model delta sigma weight residual 139.87 119.50 20.37 1.00e+00 1.00e+00 4.15e+02 angle pdb=" PA ATP M 501 " pdb=" O3A ATP M 501 " pdb=" PB ATP M 501 " ideal model delta sigma weight residual 136.83 119.24 17.59 1.00e+00 1.00e+00 3.10e+02 angle pdb=" PA ATP L 501 " pdb=" O3A ATP L 501 " pdb=" PB ATP L 501 " ideal model delta sigma weight residual 136.83 119.72 17.11 1.00e+00 1.00e+00 2.93e+02 angle pdb=" PB ATP I 501 " pdb=" O3B ATP I 501 " pdb=" PG ATP I 501 " ideal model delta sigma weight residual 139.87 124.06 15.81 1.00e+00 1.00e+00 2.50e+02 angle pdb=" PB ATP K 501 " pdb=" O3B ATP K 501 " pdb=" PG ATP K 501 " ideal model delta sigma weight residual 139.87 124.58 15.29 1.00e+00 1.00e+00 2.34e+02 ... (remaining 93313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.47: 39702 24.47 - 48.93: 1427 48.93 - 73.40: 494 73.40 - 97.87: 203 97.87 - 122.33: 1 Dihedral angle restraints: 41827 sinusoidal: 16832 harmonic: 24995 Sorted by residual: dihedral pdb=" CA SER I 182 " pdb=" C SER I 182 " pdb=" N ASP I 183 " pdb=" CA ASP I 183 " ideal model delta harmonic sigma weight residual 180.00 140.08 39.92 0 5.00e+00 4.00e-02 6.38e+01 dihedral pdb=" CA ASP n 77 " pdb=" C ASP n 77 " pdb=" N ASN n 78 " pdb=" CA ASN n 78 " ideal model delta harmonic sigma weight residual -180.00 -145.21 -34.79 0 5.00e+00 4.00e-02 4.84e+01 dihedral pdb=" O2A ADP J 501 " pdb=" O3A ADP J 501 " pdb=" PA ADP J 501 " pdb=" PB ADP J 501 " ideal model delta sinusoidal sigma weight residual -60.00 62.33 -122.33 1 2.00e+01 2.50e-03 3.68e+01 ... (remaining 41824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 9728 0.122 - 0.244: 679 0.244 - 0.366: 103 0.366 - 0.488: 27 0.488 - 0.610: 2 Chirality restraints: 10539 Sorted by residual: chirality pdb=" CB ILE 1 187 " pdb=" CA ILE 1 187 " pdb=" CG1 ILE 1 187 " pdb=" CG2 ILE 1 187 " both_signs ideal model delta sigma weight residual False 2.64 2.03 0.61 2.00e-01 2.50e+01 9.31e+00 chirality pdb=" CA LYS J 141 " pdb=" N LYS J 141 " pdb=" C LYS J 141 " pdb=" CB LYS J 141 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.21e+00 chirality pdb=" CB VAL 1 152 " pdb=" CA VAL 1 152 " pdb=" CG1 VAL 1 152 " pdb=" CG2 VAL 1 152 " both_signs ideal model delta sigma weight residual False -2.63 -3.12 0.49 2.00e-01 2.50e+01 5.93e+00 ... (remaining 10536 not shown) Planarity restraints: 12050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 82 " -0.159 2.00e-02 2.50e+03 1.03e-01 2.14e+02 pdb=" CG TYR B 82 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR B 82 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR B 82 " 0.084 2.00e-02 2.50e+03 pdb=" CE1 TYR B 82 " 0.084 2.00e-02 2.50e+03 pdb=" CE2 TYR B 82 " 0.079 2.00e-02 2.50e+03 pdb=" CZ TYR B 82 " 0.026 2.00e-02 2.50e+03 pdb=" OH TYR B 82 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 105 " -0.157 2.00e-02 2.50e+03 9.56e-02 1.83e+02 pdb=" CG TYR 6 105 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 105 " 0.139 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 105 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 105 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 105 " 0.076 2.00e-02 2.50e+03 pdb=" CZ TYR 6 105 " 0.031 2.00e-02 2.50e+03 pdb=" OH TYR 6 105 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 70 " 0.174 2.00e-02 2.50e+03 9.04e-02 1.63e+02 pdb=" CG TYR L 70 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR L 70 " -0.097 2.00e-02 2.50e+03 pdb=" CD2 TYR L 70 " -0.089 2.00e-02 2.50e+03 pdb=" CE1 TYR L 70 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR L 70 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR L 70 " 0.035 2.00e-02 2.50e+03 pdb=" OH TYR L 70 " 0.101 2.00e-02 2.50e+03 ... (remaining 12047 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 4 1.89 - 2.64: 576 2.64 - 3.40: 86116 3.40 - 4.15: 156019 4.15 - 4.90: 288124 Nonbonded interactions: 530839 Sorted by model distance: nonbonded pdb=" CD1 TYR n 186 " pdb=" NH1 ARG 1 29 " model vdw 1.139 3.420 nonbonded pdb=" CG2 THR L 229 " pdb="MG MG L 502 " model vdw 1.658 2.590 nonbonded pdb=" CG TYR n 186 " pdb=" NH1 ARG 1 29 " model vdw 1.664 3.340 nonbonded pdb=" O ALA D 24 " pdb=" OH TYR I 436 " model vdw 1.702 2.440 nonbonded pdb=" OE1 GLN I 393 " pdb=" O2' ATP I 501 " model vdw 1.900 2.440 ... (remaining 530834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain 'h' } ncs_group { reference = chain '2' selection = chain 'i' } ncs_group { reference = chain '3' selection = chain 'j' } ncs_group { reference = chain '4' selection = chain 'k' } ncs_group { reference = chain '5' selection = chain 'l' } ncs_group { reference = chain '6' selection = chain 'm' } ncs_group { reference = chain '7' selection = (chain 'n' and resid 1 through 229) } ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = (chain 'F' and resid 3 through 233) selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 16.190 Check model and map are aligned: 0.740 Set scattering table: 0.450 Process input model: 132.990 Find NCS groups from input model: 4.770 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 : 0.013 0.232 69044 Z= 0.870 Angle : 1.325 24.085 93318 Z= 0.820 Chirality : 0.071 0.610 10539 Planarity : 0.010 0.206 12050 Dihedral : 16.196 122.332 25821 Min Nonbonded Distance : 1.139 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 1.02 % Allowed : 5.80 % Favored : 93.18 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.07), residues: 8602 helix: -3.29 (0.06), residues: 3177 sheet: -1.27 (0.11), residues: 1774 loop : -2.40 (0.08), residues: 3651 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5035 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 4852 time to evaluate : 6.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 183 outliers final: 50 residues processed: 4914 average time/residue: 0.6985 time to fit residues: 5718.6043 Evaluate side-chains 3393 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 3343 time to evaluate : 5.894 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.5267 time to fit residues: 57.2594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 722 optimal weight: 0.9980 chunk 648 optimal weight: 0.9990 chunk 360 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 437 optimal weight: 0.7980 chunk 346 optimal weight: 0.8980 chunk 670 optimal weight: 0.9990 chunk 259 optimal weight: 0.8980 chunk 407 optimal weight: 0.6980 chunk 499 optimal weight: 3.9990 chunk 777 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 30 GLN ** b 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 93 HIS c 176 GLN e 15 GLN e 91 HIS ** e 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 146 GLN f 89 GLN f 151 ASN f 184 ASN g 114 GLN h 157 HIS i 66 HIS i 189 ASN j 63 ASN j 203 GLN k 37 GLN k 55 GLN ** k 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 89 GLN l 209 ASN m 1 GLN m 49 ASN n 2 GLN n 74 ASN n 120 GLN A 6 HIS A 47 GLN A 75 ASN A 167 GLN A 200 HIS B 241 GLN D 77 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS D 115 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN D 202 GLN E 210 GLN F 3 ASN F 20 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN ** 2 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 172 ASN 2 189 ASN 4 63 ASN 4 101 ASN 4 166 GLN 5 89 GLN 5 191 HIS 6 49 ASN 6 92 ASN 6 94 GLN 6 195 HIS ** 7 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN 7 152 ASN 7 213 GLN ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 ASN H 330 GLN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 ASN ** I 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 140 HIS K 200 GLN K 319 ASN K 375 ASN L 208 GLN L 242 ASN L 302 GLN ** L 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 GLN M 390 GLN J 52 ASN J 111 GLN J 156 GLN J 204 HIS ** J 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 69044 Z= 0.234 Angle : 0.702 11.539 93318 Z= 0.374 Chirality : 0.046 0.255 10539 Planarity : 0.005 0.093 12050 Dihedral : 6.047 85.617 9480 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.07 % Favored : 96.73 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.53 (0.08), residues: 8602 helix: -0.74 (0.08), residues: 3189 sheet: -0.41 (0.11), residues: 1764 loop : -1.45 (0.09), residues: 3649 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3984 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 3968 time to evaluate : 5.928 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 outliers start: 16 outliers final: 2 residues processed: 3970 average time/residue: 0.6900 time to fit residues: 4671.1694 Evaluate side-chains 3168 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 3166 time to evaluate : 5.992 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4869 time to fit residues: 10.0919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 432 optimal weight: 0.8980 chunk 241 optimal weight: 5.9990 chunk 646 optimal weight: 6.9990 chunk 529 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 778 optimal weight: 0.7980 chunk 841 optimal weight: 6.9990 chunk 693 optimal weight: 4.9990 chunk 772 optimal weight: 0.1980 chunk 265 optimal weight: 5.9990 chunk 624 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 6 HIS c 176 GLN c 226 GLN d 14 HIS d 17 GLN d 53 GLN e 91 HIS ** f 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 114 GLN g 178 HIS h 69 GLN h 92 ASN ** h 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 66 HIS l 66 HIS m 1 GLN m 92 ASN n 2 GLN n 74 ASN A 28 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN D 38 ASN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS D 120 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 GLN 2 85 GLN 2 141 HIS ** 3 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 37 GLN 4 166 GLN 4 191 GLN 5 89 GLN 5 188 HIS ** 5 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 155 ASN 6 195 HIS 7 2 GLN 7 18 ASN ** 7 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 112 ASN 7 213 GLN ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 HIS ** I 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 ASN ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 426 ASN ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 GLN K 414 GLN ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 302 GLN ** L 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 ASN M 74 GLN M 302 GLN J 47 GLN J 49 ASN J 52 ASN ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 269 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 69044 Z= 0.207 Angle : 0.622 11.463 93318 Z= 0.327 Chirality : 0.045 0.262 10539 Planarity : 0.004 0.063 12050 Dihedral : 5.574 83.571 9480 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.21 % Favored : 96.58 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.09), residues: 8602 helix: 0.31 (0.09), residues: 3173 sheet: -0.05 (0.12), residues: 1785 loop : -1.04 (0.10), residues: 3644 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3719 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 3712 time to evaluate : 6.052 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 outliers start: 7 outliers final: 3 residues processed: 3712 average time/residue: 0.6747 time to fit residues: 4283.4773 Evaluate side-chains 3138 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 3135 time to evaluate : 5.941 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5325 time to fit residues: 11.2173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 769 optimal weight: 0.0970 chunk 585 optimal weight: 0.9980 chunk 404 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 371 optimal weight: 2.9990 chunk 522 optimal weight: 2.9990 chunk 781 optimal weight: 20.0000 chunk 827 optimal weight: 9.9990 chunk 408 optimal weight: 4.9990 chunk 740 optimal weight: 8.9990 chunk 222 optimal weight: 0.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 6 HIS a 32 ASN c 58 GLN c 123 GLN c 176 GLN d 53 GLN d 115 GLN ** e 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 HIS f 165 GLN f 184 ASN g 19 GLN g 114 GLN h 69 GLN ** h 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 81 GLN i 85 GLN i 144 GLN ** i 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 31 GLN ** j 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 37 GLN l 209 ASN m 1 GLN ** m 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 179 ASN A 30 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 HIS ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN C 30 HIS C 155 ASN D 17 GLN D 77 ASN D 94 HIS ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 GLN ** 1 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 69 GLN 2 85 GLN 2 109 HIS ** 3 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 133 HIS 4 147 HIS 6 8 ASN ** 6 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 165 ASN 7 61 GLN 7 74 ASN ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 HIS I 238 ASN I 274 ASN ** I 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 ASN K 72 GLN ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 ASN K 244 HIS L 393 ASN J 52 ASN J 111 GLN J 170 HIS J 336 ASN J 379 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 69044 Z= 0.253 Angle : 0.615 11.293 93318 Z= 0.323 Chirality : 0.045 0.251 10539 Planarity : 0.004 0.056 12050 Dihedral : 5.341 85.414 9480 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.16 % Favored : 96.68 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.09), residues: 8602 helix: 0.73 (0.09), residues: 3171 sheet: -0.06 (0.12), residues: 1822 loop : -0.81 (0.10), residues: 3609 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3613 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 3601 time to evaluate : 5.939 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 outliers start: 12 outliers final: 4 residues processed: 3604 average time/residue: 0.6404 time to fit residues: 3929.9811 Evaluate side-chains 3055 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 3051 time to evaluate : 5.889 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5341 time to fit residues: 12.0761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 689 optimal weight: 7.9990 chunk 469 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 616 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 chunk 706 optimal weight: 2.9990 chunk 571 optimal weight: 0.0030 chunk 0 optimal weight: 5.9990 chunk 422 optimal weight: 7.9990 chunk 742 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 6 HIS a 32 ASN c 58 GLN c 176 GLN d 115 GLN ** e 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 83 HIS ** e 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 114 GLN g 119 HIS h 141 ASN h 161 GLN i 144 GLN ** i 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 65 GLN ** k 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 188 HIS m 1 GLN ** m 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 92 ASN m 94 GLN n 2 GLN n 74 ASN n 120 GLN n 149 HIS B 218 ASN C 30 HIS C 232 GLN D 68 HIS D 94 HIS E 149 HIS F 99 ASN ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 28 ASN 1 69 GLN ** 1 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 156 ASN ** 3 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 37 GLN 4 65 GLN 4 133 HIS 5 89 GLN 6 36 ASN ** 6 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 165 ASN ** 6 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 61 GLN 7 74 ASN 7 152 ASN ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 HIS ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 ASN K 244 HIS ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 302 GLN L 311 GLN L 387 ASN L 393 ASN M 302 GLN ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 170 HIS J 379 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 69044 Z= 0.252 Angle : 0.616 10.681 93318 Z= 0.322 Chirality : 0.045 0.249 10539 Planarity : 0.004 0.069 12050 Dihedral : 5.254 85.350 9480 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.65 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.09), residues: 8602 helix: 0.90 (0.09), residues: 3162 sheet: 0.06 (0.12), residues: 1793 loop : -0.78 (0.10), residues: 3647 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3573 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 3568 time to evaluate : 5.990 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: 5 outliers final: 0 residues processed: 3570 average time/residue: 0.6493 time to fit residues: 3969.4959 Evaluate side-chains 3026 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3026 time to evaluate : 6.020 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.3188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 278 optimal weight: 0.4980 chunk 745 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 485 optimal weight: 0.2980 chunk 204 optimal weight: 2.9990 chunk 828 optimal weight: 10.0000 chunk 687 optimal weight: 0.2980 chunk 383 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 273 optimal weight: 0.5980 chunk 434 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 6 HIS c 58 GLN c 176 GLN d 115 GLN ** e 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 99 ASN f 118 ASN f 165 GLN g 114 GLN g 224 HIS h 69 GLN h 161 GLN i 62 ASN i 144 GLN k 65 GLN l 166 HIS m 1 GLN ** m 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 92 ASN m 95 HIS n 179 ASN ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS B 218 ASN C 30 HIS E 106 GLN F 99 ASN ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 160 GLN 3 172 ASN 4 65 GLN ** 4 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 36 ASN ** 6 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 94 GLN 6 165 ASN ** 6 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 2 GLN 7 61 GLN 7 74 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 ASN K 244 HIS ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 ASN J 331 HIS J 379 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 69044 Z= 0.173 Angle : 0.598 10.007 93318 Z= 0.310 Chirality : 0.044 0.267 10539 Planarity : 0.004 0.077 12050 Dihedral : 5.098 85.877 9480 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.91 % Favored : 96.94 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.09), residues: 8602 helix: 1.07 (0.09), residues: 3164 sheet: 0.09 (0.12), residues: 1788 loop : -0.70 (0.10), residues: 3650 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3652 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 3646 time to evaluate : 5.972 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 outliers start: 6 outliers final: 3 residues processed: 3648 average time/residue: 0.6593 time to fit residues: 4105.8150 Evaluate side-chains 3079 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 3076 time to evaluate : 5.916 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5001 time to fit residues: 11.0440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 798 optimal weight: 9.9990 chunk 93 optimal weight: 0.0070 chunk 471 optimal weight: 6.9990 chunk 604 optimal weight: 0.9980 chunk 468 optimal weight: 0.9980 chunk 697 optimal weight: 5.9990 chunk 462 optimal weight: 2.9990 chunk 825 optimal weight: 4.9990 chunk 516 optimal weight: 4.9990 chunk 503 optimal weight: 0.6980 chunk 380 optimal weight: 6.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 6 HIS c 58 GLN c 176 GLN ** c 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** e 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 180 HIS ** g 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 GLN h 161 GLN ** i 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 65 GLN m 1 GLN m 36 ASN ** m 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 92 ASN ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN C 30 HIS ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 ASN ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 189 ASN 4 37 GLN 4 65 GLN 4 133 HIS 6 36 ASN ** 6 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 2 GLN 7 3 GLN 7 62 HIS 7 74 ASN 7 152 ASN H 98 GLN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 302 GLN L 387 ASN M 253 GLN M 302 GLN ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 379 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 69044 Z= 0.220 Angle : 0.607 11.463 93318 Z= 0.316 Chirality : 0.044 0.265 10539 Planarity : 0.004 0.079 12050 Dihedral : 5.050 86.292 9480 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.10 % Favored : 96.76 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.09), residues: 8602 helix: 1.07 (0.09), residues: 3192 sheet: 0.12 (0.12), residues: 1801 loop : -0.65 (0.10), residues: 3609 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3505 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 3502 time to evaluate : 5.970 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 outliers start: 3 outliers final: 2 residues processed: 3502 average time/residue: 0.6491 time to fit residues: 3883.2809 Evaluate side-chains 2998 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2996 time to evaluate : 5.963 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5256 time to fit residues: 10.1607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 510 optimal weight: 0.2980 chunk 329 optimal weight: 4.9990 chunk 492 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 162 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 524 optimal weight: 0.7980 chunk 562 optimal weight: 2.9990 chunk 407 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 648 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 6 HIS c 58 GLN c 176 GLN ** c 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 92 ASN f 99 ASN f 165 GLN g 166 GLN ** h 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 161 GLN m 1 GLN n 179 ASN A 32 ASN B 218 ASN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 GLN F 99 ASN ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 66 HIS ** 2 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 37 GLN 4 133 HIS 6 36 ASN ** 6 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 2 GLN 7 74 ASN 7 102 GLN 7 152 ASN ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 ASN K 98 GLN K 200 GLN K 238 ASN ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 302 GLN L 387 ASN J 379 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 69044 Z= 0.189 Angle : 0.608 11.352 93318 Z= 0.314 Chirality : 0.044 0.372 10539 Planarity : 0.004 0.061 12050 Dihedral : 4.951 87.030 9480 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.00 % Favored : 96.87 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.09), residues: 8602 helix: 1.14 (0.09), residues: 3202 sheet: 0.14 (0.12), residues: 1771 loop : -0.63 (0.10), residues: 3629 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3509 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 3506 time to evaluate : 5.967 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 outliers start: 3 outliers final: 1 residues processed: 3507 average time/residue: 0.6491 time to fit residues: 3896.2124 Evaluate side-chains 2997 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2996 time to evaluate : 5.894 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5121 time to fit residues: 9.1559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 750 optimal weight: 6.9990 chunk 790 optimal weight: 3.9990 chunk 721 optimal weight: 5.9990 chunk 768 optimal weight: 0.9990 chunk 462 optimal weight: 0.8980 chunk 334 optimal weight: 0.9990 chunk 603 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 694 optimal weight: 0.0370 chunk 727 optimal weight: 0.6980 chunk 766 optimal weight: 9.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 6 HIS c 58 GLN c 176 GLN ** c 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN d 176 ASN ** f 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 99 ASN f 118 ASN g 166 GLN ** h 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 161 GLN ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 66 HIS ** i 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 37 GLN k 65 GLN ** k 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 24 ASN m 1 GLN ** m 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 92 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN C 30 HIS ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN G 119 HIS ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 GLN 1 62 HIS ** 1 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 172 ASN 2 189 ASN 4 37 GLN 4 65 GLN ** 4 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 36 ASN ** 6 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 165 ASN ** 6 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 2 GLN 7 74 ASN H 98 GLN ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 ASN ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 ASN I 365 HIS K 98 GLN K 238 ASN K 244 HIS ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 253 GLN J 379 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 69044 Z= 0.193 Angle : 0.619 11.289 93318 Z= 0.319 Chirality : 0.044 0.297 10539 Planarity : 0.004 0.062 12050 Dihedral : 4.940 87.531 9480 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.98 % Favored : 96.90 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.09), residues: 8602 helix: 1.15 (0.09), residues: 3209 sheet: 0.17 (0.12), residues: 1761 loop : -0.63 (0.10), residues: 3632 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3463 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 3460 time to evaluate : 6.067 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 outliers start: 3 outliers final: 2 residues processed: 3461 average time/residue: 0.6549 time to fit residues: 3884.3829 Evaluate side-chains 2977 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2975 time to evaluate : 6.110 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5399 time to fit residues: 10.4805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 504 optimal weight: 0.8980 chunk 812 optimal weight: 3.9990 chunk 496 optimal weight: 4.9990 chunk 385 optimal weight: 0.8980 chunk 565 optimal weight: 3.9990 chunk 852 optimal weight: 5.9990 chunk 784 optimal weight: 3.9990 chunk 679 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 524 optimal weight: 0.0980 chunk 416 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 6 HIS ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 ASN c 58 GLN c 176 GLN c 226 GLN d 176 ASN ** e 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 106 GLN f 99 ASN f 118 ASN f 165 GLN g 166 GLN ** h 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 62 ASN ** i 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 37 GLN k 65 GLN l 24 ASN l 53 GLN m 1 GLN m 92 ASN A 32 ASN B 218 ASN C 232 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 65 GLN 4 133 HIS 5 89 GLN 6 36 ASN ** 6 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN ** 7 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 ASN ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 ASN I 393 GLN I 426 ASN K 98 GLN K 142 HIS K 200 GLN K 238 ASN K 414 GLN ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 302 GLN J 123 HIS J 379 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.6683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 69044 Z= 0.263 Angle : 0.644 11.177 93318 Z= 0.334 Chirality : 0.045 0.279 10539 Planarity : 0.004 0.061 12050 Dihedral : 4.997 88.195 9480 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.36 % Favored : 96.51 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.09), residues: 8602 helix: 1.12 (0.09), residues: 3215 sheet: 0.13 (0.12), residues: 1762 loop : -0.64 (0.10), residues: 3625 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3417 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 3414 time to evaluate : 6.042 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 outliers start: 3 outliers final: 1 residues processed: 3415 average time/residue: 0.6506 time to fit residues: 3807.1865 Evaluate side-chains 2919 residues out of total 7336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2918 time to evaluate : 5.920 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4927 time to fit residues: 9.1696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 539 optimal weight: 0.9980 chunk 723 optimal weight: 0.0970 chunk 208 optimal weight: 5.9990 chunk 626 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 680 optimal weight: 0.9980 chunk 284 optimal weight: 0.6980 chunk 698 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 6 HIS ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 58 GLN c 176 GLN d 115 GLN d 176 ASN ** e 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 99 ASN g 166 GLN ** h 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 62 ASN i 81 GLN ** i 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 37 GLN l 24 ASN l 166 HIS m 1 GLN m 92 ASN A 32 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN C 30 HIS C 58 GLN D 53 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 161 GLN 2 189 ASN 4 37 GLN 4 65 GLN ** 4 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 89 GLN 6 36 ASN ** 6 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 ASN ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 ASN ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 GLN K 238 ASN ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 379 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.131288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.099663 restraints weight = 112093.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.103003 restraints weight = 62109.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.105262 restraints weight = 40850.859| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.6854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 69044 Z= 0.195 Angle : 0.631 11.091 93318 Z= 0.325 Chirality : 0.045 0.273 10539 Planarity : 0.004 0.048 12050 Dihedral : 4.939 89.252 9480 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.27 % Favored : 96.62 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.09), residues: 8602 helix: 1.18 (0.09), residues: 3207 sheet: 0.11 (0.12), residues: 1744 loop : -0.63 (0.10), residues: 3651 =============================================================================== Job complete usr+sys time: 46586.27 seconds wall clock time: 799 minutes 10.66 seconds (47950.66 seconds total)