Starting phenix.real_space_refine on Sun Mar 10 14:20:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5j_11645/03_2024/7a5j_11645_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5j_11645/03_2024/7a5j_11645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5j_11645/03_2024/7a5j_11645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5j_11645/03_2024/7a5j_11645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5j_11645/03_2024/7a5j_11645_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5j_11645/03_2024/7a5j_11645_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.013 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: 9 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1693 5.49 5 Mg 92 5.21 5 S 292 5.16 5 Cl 2 4.86 5 Na 4 4.78 5 C 60813 2.51 5 N 19305 2.21 5 O 23928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 138": "OD1" <-> "OD2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ASP 161": "OD1" <-> "OD2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E ASP 126": "OD1" <-> "OD2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 301": "OD1" <-> "OD2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "E ASP 331": "OD1" <-> "OD2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 94": "OD1" <-> "OD2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F ASP 191": "OD1" <-> "OD2" Residue "F ASP 214": "OD1" <-> "OD2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F ASP 271": "OD1" <-> "OD2" Residue "F ASP 277": "OD1" <-> "OD2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H GLU 142": "OE1" <-> "OE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "I ARG 83": "NH1" <-> "NH2" Residue "I ASP 92": "OD1" <-> "OD2" Residue "I GLU 107": "OE1" <-> "OE2" Residue "I PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 158": "OE1" <-> "OE2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J ASP 59": "OD1" <-> "OD2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "J ASP 75": "OD1" <-> "OD2" Residue "J GLU 79": "OE1" <-> "OE2" Residue "J PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 119": "OE1" <-> "OE2" Residue "J ASP 127": "OD1" <-> "OD2" Residue "J GLU 128": "OE1" <-> "OE2" Residue "J PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ASP 22": "OD1" <-> "OD2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K ARG 118": "NH1" <-> "NH2" Residue "K GLU 131": "OE1" <-> "OE2" Residue "K GLU 135": "OE1" <-> "OE2" Residue "K GLU 143": "OE1" <-> "OE2" Residue "K GLU 161": "OE1" <-> "OE2" Residue "K ASP 175": "OD1" <-> "OD2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "L ARG 37": "NH1" <-> "NH2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L ARG 99": "NH1" <-> "NH2" Residue "L ASP 101": "OD1" <-> "OD2" Residue "L ASP 110": "OD1" <-> "OD2" Residue "L ARG 118": "NH1" <-> "NH2" Residue "L ARG 128": "NH1" <-> "NH2" Residue "L ARG 130": "NH1" <-> "NH2" Residue "M ASP 14": "OD1" <-> "OD2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 57": "NH1" <-> "NH2" Residue "M ARG 62": "NH1" <-> "NH2" Residue "M GLU 85": "OE1" <-> "OE2" Residue "M ASP 106": "OD1" <-> "OD2" Residue "M ASP 111": "OD1" <-> "OD2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M ASP 146": "OD1" <-> "OD2" Residue "M ASP 180": "OD1" <-> "OD2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M GLU 235": "OE1" <-> "OE2" Residue "M GLU 251": "OE1" <-> "OE2" Residue "M ARG 259": "NH1" <-> "NH2" Residue "M ASP 287": "OD1" <-> "OD2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N GLU 65": "OE1" <-> "OE2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "N ASP 148": "OD1" <-> "OD2" Residue "N GLU 168": "OE1" <-> "OE2" Residue "N GLU 171": "OE1" <-> "OE2" Residue "N PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 177": "OD1" <-> "OD2" Residue "N PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O GLU 57": "OE1" <-> "OE2" Residue "O TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O ARG 137": "NH1" <-> "NH2" Residue "O ARG 138": "NH1" <-> "NH2" Residue "O ASP 139": "OD1" <-> "OD2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "O ASP 155": "OD1" <-> "OD2" Residue "P GLU 47": "OE1" <-> "OE2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 75": "NH1" <-> "NH2" Residue "P ARG 80": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "P GLU 138": "OE1" <-> "OE2" Residue "P GLU 152": "OE1" <-> "OE2" Residue "P ASP 156": "OD1" <-> "OD2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "Q ARG 74": "NH1" <-> "NH2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q ARG 86": "NH1" <-> "NH2" Residue "Q ARG 143": "NH1" <-> "NH2" Residue "Q GLU 156": "OE1" <-> "OE2" Residue "Q GLU 173": "OE1" <-> "OE2" Residue "Q GLU 180": "OE1" <-> "OE2" Residue "Q ARG 191": "NH1" <-> "NH2" Residue "Q ASP 201": "OD1" <-> "OD2" Residue "Q GLU 210": "OE1" <-> "OE2" Residue "Q ARG 244": "NH1" <-> "NH2" Residue "Q ARG 271": "NH1" <-> "NH2" Residue "Q GLU 272": "OE1" <-> "OE2" Residue "Q ASP 274": "OD1" <-> "OD2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R ARG 122": "NH1" <-> "NH2" Residue "R ARG 123": "NH1" <-> "NH2" Residue "R ASP 134": "OD1" <-> "OD2" Residue "R GLU 137": "OE1" <-> "OE2" Residue "R GLU 139": "OE1" <-> "OE2" Residue "R PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 68": "OD1" <-> "OD2" Residue "S TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 104": "NH1" <-> "NH2" Residue "S ASP 112": "OD1" <-> "OD2" Residue "S ASP 121": "OD1" <-> "OD2" Residue "S ASP 139": "OD1" <-> "OD2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "S ARG 184": "NH1" <-> "NH2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "T GLU 123": "OE1" <-> "OE2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ASP 131": "OD1" <-> "OD2" Residue "T ARG 149": "NH1" <-> "NH2" Residue "T ARG 157": "NH1" <-> "NH2" Residue "T TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 187": "OE1" <-> "OE2" Residue "U PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 30": "NH1" <-> "NH2" Residue "U GLU 37": "OE1" <-> "OE2" Residue "U ASP 38": "OD1" <-> "OD2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U ARG 71": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U ARG 83": "NH1" <-> "NH2" Residue "U TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 132": "OE1" <-> "OE2" Residue "U ARG 143": "NH1" <-> "NH2" Residue "V ARG 20": "NH1" <-> "NH2" Residue "V TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 31": "OD1" <-> "OD2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "V ASP 51": "OD1" <-> "OD2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "V ASP 53": "OD1" <-> "OD2" Residue "V TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 63": "OE1" <-> "OE2" Residue "V ASP 69": "OD1" <-> "OD2" Residue "V ARG 96": "NH1" <-> "NH2" Residue "V ARG 118": "NH1" <-> "NH2" Residue "V ASP 127": "OD1" <-> "OD2" Residue "V PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 142": "OE1" <-> "OE2" Residue "V ARG 145": "NH1" <-> "NH2" Residue "V ASP 176": "OD1" <-> "OD2" Residue "V ARG 185": "NH1" <-> "NH2" Residue "V GLU 200": "OE1" <-> "OE2" Residue "V GLU 206": "OE1" <-> "OE2" Residue "V TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W ARG 109": "NH1" <-> "NH2" Residue "W ASP 115": "OD1" <-> "OD2" Residue "W TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X GLU 33": "OE1" <-> "OE2" Residue "X ARG 59": "NH1" <-> "NH2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X GLU 111": "OE1" <-> "OE2" Residue "X ASP 133": "OD1" <-> "OD2" Residue "X ASP 152": "OD1" <-> "OD2" Residue "X ARG 163": "NH1" <-> "NH2" Residue "X ASP 173": "OD1" <-> "OD2" Residue "X ARG 184": "NH1" <-> "NH2" Residue "X GLU 193": "OE1" <-> "OE2" Residue "X GLU 198": "OE1" <-> "OE2" Residue "X GLU 199": "OE1" <-> "OE2" Residue "X GLU 209": "OE1" <-> "OE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X GLU 220": "OE1" <-> "OE2" Residue "X PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 66": "OE1" <-> "OE2" Residue "Y ASP 70": "OD1" <-> "OD2" Residue "Y ARG 91": "NH1" <-> "NH2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Y ASP 97": "OD1" <-> "OD2" Residue "Y ARG 109": "NH1" <-> "NH2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "Y ASP 133": "OD1" <-> "OD2" Residue "Y ASP 140": "OD1" <-> "OD2" Residue "Y GLU 150": "OE1" <-> "OE2" Residue "Y GLU 161": "OE1" <-> "OE2" Residue "Y ARG 175": "NH1" <-> "NH2" Residue "Y ARG 196": "NH1" <-> "NH2" Residue "Y ASP 206": "OD1" <-> "OD2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "Y GLU 212": "OE1" <-> "OE2" Residue "Z GLU 43": "OE1" <-> "OE2" Residue "Z ASP 52": "OD1" <-> "OD2" Residue "Z ASP 84": "OD1" <-> "OD2" Residue "Z GLU 92": "OE1" <-> "OE2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "0 GLU 88": "OE1" <-> "OE2" Residue "0 ASP 108": "OD1" <-> "OD2" Residue "0 TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 136": "OE1" <-> "OE2" Residue "0 TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 178": "OD1" <-> "OD2" Residue "0 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 19": "NH1" <-> "NH2" Residue "1 ARG 34": "NH1" <-> "NH2" Residue "1 GLU 58": "OE1" <-> "OE2" Residue "2 ARG 49": "NH1" <-> "NH2" Residue "2 ARG 69": "NH1" <-> "NH2" Residue "3 ARG 104": "NH1" <-> "NH2" Residue "3 ASP 112": "OD1" <-> "OD2" Residue "3 ARG 116": "NH1" <-> "NH2" Residue "3 ARG 125": "NH1" <-> "NH2" Residue "3 ARG 168": "NH1" <-> "NH2" Residue "3 ASP 174": "OD1" <-> "OD2" Residue "3 ASP 175": "OD1" <-> "OD2" Residue "3 ARG 183": "NH1" <-> "NH2" Residue "5 ASP 47": "OD1" <-> "OD2" Residue "5 GLU 56": "OE1" <-> "OE2" Residue "5 ASP 84": "OD1" <-> "OD2" Residue "5 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 115": "OE1" <-> "OE2" Residue "5 ARG 162": "NH1" <-> "NH2" Residue "5 GLU 169": "OE1" <-> "OE2" Residue "5 ASP 182": "OD1" <-> "OD2" Residue "5 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 223": "NH1" <-> "NH2" Residue "5 ASP 234": "OD1" <-> "OD2" Residue "5 GLU 244": "OE1" <-> "OE2" Residue "5 GLU 246": "OE1" <-> "OE2" Residue "5 ASP 264": "OD1" <-> "OD2" Residue "5 ASP 272": "OD1" <-> "OD2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 348": "OD1" <-> "OD2" Residue "5 ARG 350": "NH1" <-> "NH2" Residue "5 PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 368": "OE1" <-> "OE2" Residue "5 ASP 379": "OD1" <-> "OD2" Residue "5 PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 409": "OE1" <-> "OE2" Residue "6 ARG 27": "NH1" <-> "NH2" Residue "6 ASP 39": "OD1" <-> "OD2" Residue "6 GLU 46": "OE1" <-> "OE2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "6 ARG 58": "NH1" <-> "NH2" Residue "6 ARG 60": "NH1" <-> "NH2" Residue "6 GLU 62": "OE1" <-> "OE2" Residue "6 GLU 64": "OE1" <-> "OE2" Residue "6 ARG 72": "NH1" <-> "NH2" Residue "6 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 124": "NH1" <-> "NH2" Residue "6 ARG 136": "NH1" <-> "NH2" Residue "6 GLU 153": "OE1" <-> "OE2" Residue "6 ARG 159": "NH1" <-> "NH2" Residue "6 ASP 160": "OD1" <-> "OD2" Residue "6 GLU 181": "OE1" <-> "OE2" Residue "6 ASP 182": "OD1" <-> "OD2" Residue "6 ASP 183": "OD1" <-> "OD2" Residue "6 GLU 207": "OE1" <-> "OE2" Residue "6 GLU 209": "OE1" <-> "OE2" Residue "6 GLU 227": "OE1" <-> "OE2" Residue "6 ASP 229": "OD1" <-> "OD2" Residue "6 ARG 261": "NH1" <-> "NH2" Residue "6 PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 296": "NH1" <-> "NH2" Residue "6 ARG 299": "NH1" <-> "NH2" Residue "6 ASP 302": "OD1" <-> "OD2" Residue "6 ARG 322": "NH1" <-> "NH2" Residue "6 ARG 364": "NH1" <-> "NH2" Residue "6 ASP 371": "OD1" <-> "OD2" Residue "6 TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 39": "OE1" <-> "OE2" Residue "7 ASP 46": "OD1" <-> "OD2" Residue "7 GLU 51": "OE1" <-> "OE2" Residue "7 GLU 63": "OE1" <-> "OE2" Residue "7 GLU 124": "OE1" <-> "OE2" Residue "7 GLU 137": "OE1" <-> "OE2" Residue "7 GLU 161": "OE1" <-> "OE2" Residue "7 ARG 168": "NH1" <-> "NH2" Residue "7 GLU 197": "OE1" <-> "OE2" Residue "7 ASP 205": "OD1" <-> "OD2" Residue "7 ASP 213": "OD1" <-> "OD2" Residue "7 GLU 217": "OE1" <-> "OE2" Residue "7 GLU 220": "OE1" <-> "OE2" Residue "7 GLU 228": "OE1" <-> "OE2" Residue "7 TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 238": "OD1" <-> "OD2" Residue "7 GLU 241": "OE1" <-> "OE2" Residue "7 GLU 242": "OE1" <-> "OE2" Residue "7 GLU 249": "OE1" <-> "OE2" Residue "7 ARG 250": "NH1" <-> "NH2" Residue "7 ARG 271": "NH1" <-> "NH2" Residue "7 GLU 279": "OE1" <-> "OE2" Residue "7 ASP 314": "OD1" <-> "OD2" Residue "8 GLU 100": "OE1" <-> "OE2" Residue "8 GLU 105": "OE1" <-> "OE2" Residue "8 ARG 137": "NH1" <-> "NH2" Residue "8 GLU 141": "OE1" <-> "OE2" Residue "8 GLU 145": "OE1" <-> "OE2" Residue "8 GLU 148": "OE1" <-> "OE2" Residue "8 GLU 149": "OE1" <-> "OE2" Residue "8 GLU 160": "OE1" <-> "OE2" Residue "8 PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 25": "NH1" <-> "NH2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 49": "NH1" <-> "NH2" Residue "9 GLU 55": "OE1" <-> "OE2" Residue "9 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 124": "OE1" <-> "OE2" Residue "9 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 54": "OD1" <-> "OD2" Residue "a ASP 66": "OD1" <-> "OD2" Residue "a GLU 70": "OE1" <-> "OE2" Residue "a GLU 105": "OE1" <-> "OE2" Residue "a GLU 110": "OE1" <-> "OE2" Residue "a ARG 122": "NH1" <-> "NH2" Residue "a ARG 128": "NH1" <-> "NH2" Residue "a ARG 131": "NH1" <-> "NH2" Residue "a ARG 133": "NH1" <-> "NH2" Residue "a ARG 142": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 41": "NH1" <-> "NH2" Residue "b GLU 45": "OE1" <-> "OE2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "b GLU 86": "OE1" <-> "OE2" Residue "b GLU 87": "OE1" <-> "OE2" Residue "b GLU 95": "OE1" <-> "OE2" Residue "b ASP 111": "OD1" <-> "OD2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 146": "NH1" <-> "NH2" Residue "c GLU 44": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ASP 67": "OD1" <-> "OD2" Residue "c GLU 71": "OE1" <-> "OE2" Residue "c PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 102": "OE1" <-> "OE2" Residue "c GLU 124": "OE1" <-> "OE2" Residue "c ASP 158": "OD1" <-> "OD2" Residue "c ARG 216": "NH1" <-> "NH2" Residue "c GLU 227": "OE1" <-> "OE2" Residue "c GLU 244": "OE1" <-> "OE2" Residue "c TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 287": "OE1" <-> "OE2" Residue "c PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 309": "OE1" <-> "OE2" Residue "d GLU 55": "OE1" <-> "OE2" Residue "d GLU 70": "OE1" <-> "OE2" Residue "d ASP 73": "OD1" <-> "OD2" Residue "d ARG 74": "NH1" <-> "NH2" Residue "d ASP 86": "OD1" <-> "OD2" Residue "d ASP 127": "OD1" <-> "OD2" Residue "d ASP 129": "OD1" <-> "OD2" Residue "d GLU 139": "OE1" <-> "OE2" Residue "d ASP 143": "OD1" <-> "OD2" Residue "d ASP 156": "OD1" <-> "OD2" Residue "d ARG 159": "NH1" <-> "NH2" Residue "d ASP 175": "OD1" <-> "OD2" Residue "d GLU 190": "OE1" <-> "OE2" Residue "d TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 226": "OD1" <-> "OD2" Residue "d ASP 241": "OD1" <-> "OD2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 69": "OE1" <-> "OE2" Residue "e ASP 93": "OD1" <-> "OD2" Residue "e GLU 125": "OE1" <-> "OE2" Residue "e GLU 139": "OE1" <-> "OE2" Residue "e GLU 142": "OE1" <-> "OE2" Residue "e ASP 167": "OD1" <-> "OD2" Residue "e GLU 189": "OE1" <-> "OE2" Residue "e GLU 201": "OE1" <-> "OE2" Residue "e ASP 258": "OD1" <-> "OD2" Residue "e GLU 259": "OE1" <-> "OE2" Residue "e ASP 278": "OD1" <-> "OD2" Residue "f TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 66": "OE1" <-> "OE2" Residue "f ASP 85": "OD1" <-> "OD2" Residue "f GLU 87": "OE1" <-> "OE2" Residue "f TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 154": "OE1" <-> "OE2" Residue "f GLU 172": "OE1" <-> "OE2" Residue "f GLU 188": "OE1" <-> "OE2" Residue "g ARG 90": "NH1" <-> "NH2" Residue "g ARG 105": "NH1" <-> "NH2" Residue "g ASP 116": "OD1" <-> "OD2" Residue "h GLU 64": "OE1" <-> "OE2" Residue "h ARG 69": "NH1" <-> "NH2" Residue "h ASP 88": "OD1" <-> "OD2" Residue "h ASP 106": "OD1" <-> "OD2" Residue "h ASP 107": "OD1" <-> "OD2" Residue "h ARG 116": "NH1" <-> "NH2" Residue "h ASP 136": "OD1" <-> "OD2" Residue "i ARG 46": "NH1" <-> "NH2" Residue "i GLU 49": "OE1" <-> "OE2" Residue "i ASP 58": "OD1" <-> "OD2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "i ARG 93": "NH1" <-> "NH2" Residue "i TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ARG 28": "NH1" <-> "NH2" Residue "j TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 65": "NH1" <-> "NH2" Residue "j ARG 66": "NH1" <-> "NH2" Residue "j ARG 76": "NH1" <-> "NH2" Residue "j ARG 94": "NH1" <-> "NH2" Residue "j GLU 101": "OE1" <-> "OE2" Residue "j ARG 103": "NH1" <-> "NH2" Residue "j GLU 106": "OE1" <-> "OE2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k ARG 31": "NH1" <-> "NH2" Residue "k GLU 40": "OE1" <-> "OE2" Residue "k PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 70": "OD1" <-> "OD2" Residue "k ARG 77": "NH1" <-> "NH2" Residue "k GLU 85": "OE1" <-> "OE2" Residue "l ARG 115": "NH1" <-> "NH2" Residue "l ARG 120": "NH1" <-> "NH2" Residue "l ARG 128": "NH1" <-> "NH2" Residue "l ARG 131": "NH1" <-> "NH2" Residue "m ASP 34": "OD1" <-> "OD2" Residue "m ASP 60": "OD1" <-> "OD2" Residue "o ARG 23": "NH1" <-> "NH2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 68": "NH1" <-> "NH2" Residue "o GLU 69": "OE1" <-> "OE2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "p ASP 46": "OD1" <-> "OD2" Residue "p ASP 56": "OD1" <-> "OD2" Residue "p ASP 74": "OD1" <-> "OD2" Residue "p GLU 100": "OE1" <-> "OE2" Residue "p ASP 149": "OD1" <-> "OD2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 38": "NH1" <-> "NH2" Residue "q GLU 43": "OE1" <-> "OE2" Residue "q ARG 63": "NH1" <-> "NH2" Residue "q GLU 80": "OE1" <-> "OE2" Residue "q GLU 89": "OE1" <-> "OE2" Residue "q GLU 101": "OE1" <-> "OE2" Residue "q GLU 110": "OE1" <-> "OE2" Residue "q ARG 114": "NH1" <-> "NH2" Residue "q GLU 123": "OE1" <-> "OE2" Residue "q GLU 141": "OE1" <-> "OE2" Residue "r GLU 37": "OE1" <-> "OE2" Residue "r GLU 40": "OE1" <-> "OE2" Residue "r GLU 110": "OE1" <-> "OE2" Residue "r ARG 132": "NH1" <-> "NH2" Residue "r ARG 153": "NH1" <-> "NH2" Residue "r ARG 168": "NH1" <-> "NH2" Residue "r ARG 171": "NH1" <-> "NH2" Residue "r ASP 183": "OD1" <-> "OD2" Residue "s ASP 54": "OD1" <-> "OD2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s GLU 74": "OE1" <-> "OE2" Residue "s ASP 77": "OD1" <-> "OD2" Residue "s GLU 78": "OE1" <-> "OE2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "s TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 103": "OD1" <-> "OD2" Residue "s GLU 153": "OE1" <-> "OE2" Residue "s ARG 158": "NH1" <-> "NH2" Residue "s ARG 160": "NH1" <-> "NH2" Residue "s ARG 162": "NH1" <-> "NH2" Residue "s GLU 168": "OE1" <-> "OE2" Residue "s ASP 178": "OD1" <-> "OD2" Residue "s TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 212": "NH1" <-> "NH2" Residue "s ARG 219": "NH1" <-> "NH2" Residue "s ARG 222": "NH1" <-> "NH2" Residue "s ARG 223": "NH1" <-> "NH2" Residue "s ASP 235": "OD1" <-> "OD2" Residue "s ARG 242": "NH1" <-> "NH2" Residue "s ASP 254": "OD1" <-> "OD2" Residue "s GLU 260": "OE1" <-> "OE2" Residue "s ASP 269": "OD1" <-> "OD2" Residue "s ARG 276": "NH1" <-> "NH2" Residue "s ARG 308": "NH1" <-> "NH2" Residue "s GLU 309": "OE1" <-> "OE2" Residue "s ASP 318": "OD1" <-> "OD2" Residue "s GLU 321": "OE1" <-> "OE2" Residue "s PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 384": "OD1" <-> "OD2" Residue "s ARG 389": "NH1" <-> "NH2" Residue "s ASP 407": "OD1" <-> "OD2" Residue "s ASP 415": "OD1" <-> "OD2" Residue "u PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 104": "OE1" <-> "OE2" Residue "u ASP 122": "OD1" <-> "OD2" Residue "u PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 165": "OD1" <-> "OD2" Residue "u ASP 171": "OD1" <-> "OD2" Residue "u GLU 183": "OE1" <-> "OE2" Residue "v ARG 6": "NH1" <-> "NH2" Residue "v ARG 14": "NH1" <-> "NH2" Residue "v ARG 24": "NH1" <-> "NH2" Residue "v ARG 28": "NH1" <-> "NH2" Residue "v PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 38": "OE1" <-> "OE2" Residue "v GLU 49": "OE1" <-> "OE2" Residue "w GLU 77": "OE1" <-> "OE2" Residue "w TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 94": "OD1" <-> "OD2" Residue "w GLU 96": "OE1" <-> "OE2" Residue "w PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 111": "OD1" <-> "OD2" Residue "w GLU 117": "OE1" <-> "OE2" Residue "w ASP 124": "OD1" <-> "OD2" Residue "w ASP 132": "OD1" <-> "OD2" Residue "w ASP 146": "OD1" <-> "OD2" Residue "w TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 6": "NH1" <-> "NH2" Residue "n TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 23": "OD1" <-> "OD2" Residue "n GLU 24": "OE1" <-> "OE2" Residue "n PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 38": "OD1" <-> "OD2" Residue "n ASP 55": "OD1" <-> "OD2" Residue "n ARG 73": "NH1" <-> "NH2" Residue "n GLU 85": "OE1" <-> "OE2" Residue "n GLU 88": "OE1" <-> "OE2" Residue "n ASP 92": "OD1" <-> "OD2" Residue "n GLU 98": "OE1" <-> "OE2" Residue "n ASP 105": "OD1" <-> "OD2" Residue "n ASP 109": "OD1" <-> "OD2" Residue "n ASP 118": "OD1" <-> "OD2" Residue "n PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 160": "NH1" <-> "NH2" Residue "n PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 183": "OE1" <-> "OE2" Residue "n ASP 187": "OD1" <-> "OD2" Residue "n GLU 202": "OE1" <-> "OE2" Residue "n GLU 202": "OE1" <-> "OE2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C ARG 232": "NH1" <-> "NH2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 106132 Number of models: 1 Model: "" Number of chains: 70 Chain: "D" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1842 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 12, 'TRANS': 223} Chain: "E" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2396 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 24, 'TRANS': 279} Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2013 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 21, 'TRANS': 228} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1283 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 11, 'TRANS': 146} Chain breaks: 1 Chain: "J" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1061 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain: "K" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1451 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 889 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "M" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2305 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 26, 'TRANS': 260} Chain: "N" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1654 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain: "O" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1245 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Chain: "P" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1148 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 134} Chain: "Q" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1805 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 14, 'TRANS': 202} Chain: "R" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1153 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "S" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1251 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "T" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1368 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 12, 'TRANS': 153} Chain: "U" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1218 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 139} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "V" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1624 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 18, 'TRANS': 183} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "W" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "X" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2035 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 18, 'TRANS': 224} Chain: "Y" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1517 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "Z" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 11, 'TRANS': 108} Chain: "0" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 880 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "1" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "3" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 831 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "4" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 333 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "5" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3156 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 354} Chain breaks: 1 Chain: "6" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2640 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 28, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "7" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2334 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 17, 'TRANS': 269} Chain: "8" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 890 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 97} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "9" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 107} Chain breaks: 1 Chain: "a" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 686 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 10, 'TRANS': 71} Chain breaks: 1 Chain: "b" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1178 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "c" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2217 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 258} Chain breaks: 1 Chain: "d" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1741 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 17, 'TRANS': 193} Chain breaks: 3 Chain: "e" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1762 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "f" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 915 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 113} Chain: "h" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 827 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain breaks: 1 Chain: "i" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 827 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "j" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Chain: "k" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 627 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Chain: "l" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 221 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "m" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 372 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "o" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 771 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain: "p" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1058 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 3 Chain: "q" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1076 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 14, 'TRANS': 113} Chain: "r" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1203 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 16, 'TRANS': 129} Chain breaks: 2 Chain: "s" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3036 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain breaks: 1 Chain: "t" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 Chain: "u" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 927 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 588 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "w" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 659 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 1767 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 228, 1742 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 214} Conformer: "B" Number of residues, atoms: 228, 1742 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 214} bond proxies already assigned to first conformer: 1745 Chain: "A" Number of atoms: 31684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1492, 31684 Classifications: {'RNA': 1492} Modifications used: {'rna2p_pur': 162, 'rna2p_pyr': 123, 'rna3p_pur': 626, 'rna3p_pyr': 581} Link IDs: {'rna2p': 284, 'rna3p': 1207} Chain breaks: 15 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1191 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 29, 'rna3p_pyr': 26} Link IDs: {'rna2p': 1, 'rna3p': 54} Chain breaks: 4 Chain: "Y2" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 145 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 27} Link IDs: {'rna2p': 15, 'rna3p': 57} Chain: "y" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 160 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'UNK:plan-1': 32} Unresolved non-hydrogen planarities: 32 Chain: "z" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "x" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 27} Link IDs: {'rna2p': 15, 'rna3p': 57} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CL': 2, ' NA': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Unusual residues: {' MG': 90, ' NA': 1} Classifications: {'undetermined': 91} Link IDs: {None: 90} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 32143 SG CYS 0 110 165.433 147.536 190.808 1.00 0.00 S ATOM 32165 SG CYS 0 113 166.142 150.631 188.544 1.00 0.00 S ATOM 32245 SG CYS 0 123 165.248 147.451 187.006 1.00 0.00 S ATOM 32268 SG CYS 0 126 169.110 148.437 189.235 1.00 0.00 S ATOM 34507 SG CYS 4 79 89.965 70.420 169.924 1.00 0.00 S ATOM 34631 SG CYS 4 92 91.864 68.448 172.416 1.00 0.00 S ATOM 7322 SG CYS I 64 62.375 96.562 176.725 1.00 0.00 S ATOM 60954 SG CYS r 70 64.230 95.047 180.847 1.00 0.00 S ATOM 61269 SG CYS r 108 64.725 93.214 177.820 1.00 0.00 S Time building chain proxies: 42.32, per 1000 atoms: 0.40 Number of scatterers: 106132 At special positions: 0 Unit cell: (251.876, 227.948, 250.617, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 3 29.99 Cl 2 17.00 S 292 16.00 P 1693 15.00 Mg 92 11.99 Na 4 11.00 O 23928 8.00 N 19305 7.00 C 60813 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 35.09 Conformation dependent library (CDL) restraints added in 10.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " pdb=" ZN 4 200 " pdb="ZN ZN 4 200 " - pdb=" ND1 HIS 4 98 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 92 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 79 " pdb=" ZN r 301 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 70 " pdb="ZN ZN r 301 " - pdb=" SG CYS I 64 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 108 " Number of angles added : 6 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16304 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 277 helices and 80 sheets defined 40.9% alpha, 13.1% beta 391 base pairs and 937 stacking pairs defined. Time for finding SS restraints: 61.67 Creating SS restraints... Processing helix chain 'D' and resid 259 through 267 removed outlier: 3.754A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 83 Proline residue: E 59 - end of helix removed outlier: 3.532A pdb=" N LYS E 70 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 73 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix removed outlier: 3.717A pdb=" N ASP E 82 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 158 through 169 removed outlier: 3.796A pdb=" N PHE E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 168 " --> pdb=" O PHE E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.963A pdb=" N PHE E 198 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 194 through 199' Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'E' and resid 304 through 309 removed outlier: 3.793A pdb=" N LYS E 308 " --> pdb=" O LEU E 304 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASP E 309 " --> pdb=" O PRO E 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 304 through 309' Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 92 through 106 removed outlier: 3.618A pdb=" N LEU F 96 " --> pdb=" O ARG F 92 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN F 105 " --> pdb=" O MET F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 185 removed outlier: 3.594A pdb=" N LEU F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS F 181 " --> pdb=" O ALA F 177 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP F 185 " --> pdb=" O LYS F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 211 removed outlier: 3.710A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 removed outlier: 4.835A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 5.324A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 3.519A pdb=" N LEU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG F 279 " --> pdb=" O TRP F 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 79 removed outlier: 4.200A pdb=" N ARG H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 74 through 79' Processing helix chain 'H' and resid 115 through 121 Processing helix chain 'H' and resid 122 through 127 removed outlier: 3.672A pdb=" N GLN H 126 " --> pdb=" O ARG H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 147 removed outlier: 3.883A pdb=" N LYS H 138 " --> pdb=" O PRO H 134 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS H 144 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 52 removed outlier: 3.758A pdb=" N LEU I 47 " --> pdb=" O GLN I 43 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU I 52 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 66 removed outlier: 3.701A pdb=" N LEU I 65 " --> pdb=" O HIS I 61 " (cutoff:3.500A) Proline residue: I 66 - end of helix No H-bonds generated for 'chain 'I' and resid 61 through 66' Processing helix chain 'I' and resid 77 through 93 removed outlier: 3.936A pdb=" N GLN I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 120 removed outlier: 3.653A pdb=" N LEU I 116 " --> pdb=" O MET I 112 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 138 Proline residue: I 133 - end of helix removed outlier: 4.272A pdb=" N GLU I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 147 removed outlier: 3.755A pdb=" N LEU I 144 " --> pdb=" O TYR I 140 " (cutoff:3.500A) Proline residue: I 145 - end of helix No H-bonds generated for 'chain 'I' and resid 140 through 147' Processing helix chain 'I' and resid 160 through 172 removed outlier: 3.616A pdb=" N MET I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL I 171 " --> pdb=" O ILE I 167 " (cutoff:3.500A) Proline residue: I 172 - end of helix Processing helix chain 'I' and resid 187 through 197 removed outlier: 4.155A pdb=" N SER I 195 " --> pdb=" O PHE I 191 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS I 196 " --> pdb=" O ILE I 192 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU I 197 " --> pdb=" O ASN I 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 43 removed outlier: 6.709A pdb=" N LEU J 35 " --> pdb=" O PRO J 31 " (cutoff:3.500A) Proline residue: J 37 - end of helix removed outlier: 5.813A pdb=" N ARG J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY J 43 " --> pdb=" O LEU J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 3.847A pdb=" N ASP J 59 " --> pdb=" O GLU J 55 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE J 60 " --> pdb=" O ARG J 56 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS J 61 " --> pdb=" O THR J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 96 removed outlier: 3.968A pdb=" N PHE J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 125 removed outlier: 3.543A pdb=" N ILE J 120 " --> pdb=" O HIS J 116 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG J 122 " --> pdb=" O TYR J 118 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE J 123 " --> pdb=" O GLU J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 152 removed outlier: 4.511A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER J 143 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU J 151 " --> pdb=" O SER J 147 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY J 152 " --> pdb=" O ALA J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 27 through 41 removed outlier: 3.619A pdb=" N MET K 34 " --> pdb=" O LYS K 30 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG K 38 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN K 40 " --> pdb=" O SER K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 91 through 99 removed outlier: 3.827A pdb=" N ARG K 98 " --> pdb=" O GLN K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 113 Proline residue: K 113 - end of helix Processing helix chain 'K' and resid 115 through 126 removed outlier: 4.939A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU K 123 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU K 125 " --> pdb=" O MET K 121 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N HIS K 126 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 removed outlier: 4.692A pdb=" N ASN K 140 " --> pdb=" O ASP K 136 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU K 141 " --> pdb=" O ILE K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 159 removed outlier: 3.545A pdb=" N TYR K 158 " --> pdb=" O ARG K 154 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR K 159 " --> pdb=" O LEU K 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 154 through 159' Processing helix chain 'K' and resid 160 through 167 Proline residue: K 167 - end of helix Processing helix chain 'L' and resid 44 through 49 removed outlier: 3.626A pdb=" N SER L 49 " --> pdb=" O ALA L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 142 removed outlier: 5.034A pdb=" N VAL L 137 " --> pdb=" O GLU L 133 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLN L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 129 removed outlier: 3.877A pdb=" N LEU L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG L 128 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS L 129 " --> pdb=" O SER L 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 124 through 129' Processing helix chain 'M' and resid 10 through 20 removed outlier: 4.215A pdb=" N ASP M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG M 17 " --> pdb=" O LEU M 13 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 55 through 60 removed outlier: 4.378A pdb=" N ARG M 59 " --> pdb=" O GLY M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 78 removed outlier: 3.918A pdb=" N ILE M 78 " --> pdb=" O PHE M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 108 removed outlier: 3.648A pdb=" N LEU M 107 " --> pdb=" O TYR M 103 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 125 removed outlier: 3.553A pdb=" N LEU M 121 " --> pdb=" O ASP M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 171 removed outlier: 3.612A pdb=" N ILE M 167 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN M 170 " --> pdb=" O ALA M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 190 removed outlier: 3.577A pdb=" N ILE M 186 " --> pdb=" O ARG M 182 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS M 189 " --> pdb=" O ASP M 185 " (cutoff:3.500A) Proline residue: M 190 - end of helix Processing helix chain 'M' and resid 191 through 197 removed outlier: 4.061A pdb=" N ARG M 196 " --> pdb=" O PRO M 192 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY M 197 " --> pdb=" O PHE M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 216 Proline residue: M 212 - end of helix removed outlier: 4.352A pdb=" N ASP M 216 " --> pdb=" O PRO M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 241 removed outlier: 4.070A pdb=" N PHE M 229 " --> pdb=" O ASP M 225 " (cutoff:3.500A) Proline residue: M 230 - end of helix removed outlier: 3.516A pdb=" N LEU M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY M 241 " --> pdb=" O ALA M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 251 removed outlier: 4.597A pdb=" N ASP M 250 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLU M 251 " --> pdb=" O ILE M 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 246 through 251' Processing helix chain 'M' and resid 252 through 259 removed outlier: 5.017A pdb=" N THR M 258 " --> pdb=" O LYS M 254 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ARG M 259 " --> pdb=" O MET M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 287 through 296 removed outlier: 3.625A pdb=" N SER M 296 " --> pdb=" O LYS M 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 74 removed outlier: 3.701A pdb=" N ARG N 73 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 69 through 74' Processing helix chain 'N' and resid 98 through 113 removed outlier: 3.708A pdb=" N PHE N 102 " --> pdb=" O HIS N 98 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER N 112 " --> pdb=" O THR N 108 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET N 113 " --> pdb=" O ILE N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 184 removed outlier: 3.850A pdb=" N VAL N 172 " --> pdb=" O GLU N 168 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN N 178 " --> pdb=" O GLY N 174 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS N 181 " --> pdb=" O ASP N 177 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS N 182 " --> pdb=" O GLN N 178 " (cutoff:3.500A) Proline residue: N 184 - end of helix Processing helix chain 'N' and resid 191 through 209 removed outlier: 3.520A pdb=" N GLU N 196 " --> pdb=" O ARG N 192 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN N 202 " --> pdb=" O MET N 198 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN N 209 " --> pdb=" O ARG N 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 222 removed outlier: 3.765A pdb=" N ALA N 221 " --> pdb=" O ARG N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 231 removed outlier: 5.538A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 removed outlier: 4.679A pdb=" N THR N 236 " --> pdb=" O PRO N 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 39 removed outlier: 3.731A pdb=" N ILE O 26 " --> pdb=" O PRO O 22 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN O 31 " --> pdb=" O HIS O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 66 removed outlier: 4.321A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP O 61 " --> pdb=" O GLU O 57 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 81 removed outlier: 3.547A pdb=" N MET O 75 " --> pdb=" O ARG O 71 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N THR O 81 " --> pdb=" O ASP O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 98 removed outlier: 4.444A pdb=" N ILE O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 87 - end of helix removed outlier: 5.315A pdb=" N ALA O 94 " --> pdb=" O PHE O 90 " (cutoff:3.500A) Proline residue: O 95 - end of helix removed outlier: 3.673A pdb=" N LYS O 98 " --> pdb=" O ALA O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 160 removed outlier: 3.524A pdb=" N LEU O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLN O 160 " --> pdb=" O LEU O 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 60 Processing helix chain 'P' and resid 110 through 117 removed outlier: 3.923A pdb=" N LYS P 114 " --> pdb=" O TRP P 110 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU P 116 " --> pdb=" O ILE P 112 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR P 117 " --> pdb=" O LYS P 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 110 through 117' Processing helix chain 'P' and resid 121 through 140 removed outlier: 3.720A pdb=" N GLU P 138 " --> pdb=" O GLN P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 155 removed outlier: 4.139A pdb=" N ALA P 154 " --> pdb=" O PRO P 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 169 removed outlier: 3.626A pdb=" N ARG P 160 " --> pdb=" O ASP P 156 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER P 163 " --> pdb=" O LYS P 159 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU P 167 " --> pdb=" O SER P 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 82 removed outlier: 3.991A pdb=" N ILE Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Proline residue: Q 82 - end of helix No H-bonds generated for 'chain 'Q' and resid 77 through 82' Processing helix chain 'Q' and resid 88 through 106 removed outlier: 4.091A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS Q 97 " --> pdb=" O GLN Q 93 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG Q 102 " --> pdb=" O ASP Q 98 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 193 removed outlier: 4.901A pdb=" N ARG Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP Q 192 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 199 removed outlier: 4.410A pdb=" N SER Q 198 " --> pdb=" O LEU Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 removed outlier: 4.278A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 262 removed outlier: 3.566A pdb=" N GLN Q 258 " --> pdb=" O MET Q 254 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLN Q 262 " --> pdb=" O GLN Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 268 removed outlier: 4.502A pdb=" N PHE Q 267 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 290 removed outlier: 4.774A pdb=" N GLU Q 279 " --> pdb=" O THR Q 275 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA Q 281 " --> pdb=" O LYS Q 277 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU Q 285 " --> pdb=" O ALA Q 281 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS Q 290 " --> pdb=" O ILE Q 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 26 removed outlier: 3.700A pdb=" N ARG R 20 " --> pdb=" O ASP R 16 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 80 removed outlier: 3.521A pdb=" N CYS R 53 " --> pdb=" O ALA R 49 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS R 60 " --> pdb=" O ALA R 56 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS R 61 " --> pdb=" O ARG R 57 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS R 62 " --> pdb=" O TYR R 58 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG R 65 " --> pdb=" O LYS R 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA R 74 " --> pdb=" O ASN R 70 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA R 75 " --> pdb=" O ARG R 71 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS R 79 " --> pdb=" O ALA R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 removed outlier: 4.174A pdb=" N ASN R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS R 93 " --> pdb=" O ASN R 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 109 removed outlier: 3.887A pdb=" N ILE R 107 " --> pdb=" O ALA R 103 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR R 108 " --> pdb=" O ASP R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 134 removed outlier: 4.123A pdb=" N ASP R 134 " --> pdb=" O ALA R 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 90 removed outlier: 3.629A pdb=" N THR S 73 " --> pdb=" O PRO S 69 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG S 74 " --> pdb=" O VAL S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 155 removed outlier: 3.686A pdb=" N VAL S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ARG S 155 " --> pdb=" O LYS S 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 150 through 155' Processing helix chain 'T' and resid 49 through 55 removed outlier: 3.966A pdb=" N LYS T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS T 54 " --> pdb=" O LYS T 50 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN T 55 " --> pdb=" O TRP T 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 49 through 55' Processing helix chain 'T' and resid 83 through 95 removed outlier: 3.746A pdb=" N TRP T 88 " --> pdb=" O LYS T 84 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE T 94 " --> pdb=" O LEU T 90 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG T 95 " --> pdb=" O ALA T 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 109 removed outlier: 3.947A pdb=" N PHE T 108 " --> pdb=" O ALA T 104 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN T 109 " --> pdb=" O GLN T 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 131 removed outlier: 4.134A pdb=" N LYS T 115 " --> pdb=" O LYS T 111 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL T 129 " --> pdb=" O GLN T 125 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 206 removed outlier: 3.989A pdb=" N ARG T 206 " --> pdb=" O GLN T 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 59 removed outlier: 3.532A pdb=" N LEU U 53 " --> pdb=" O THR U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 125 through 137 removed outlier: 3.870A pdb=" N MET U 129 " --> pdb=" O ASP U 125 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU U 130 " --> pdb=" O LEU U 126 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU U 133 " --> pdb=" O MET U 129 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ARG U 134 " --> pdb=" O LEU U 130 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN U 136 " --> pdb=" O GLU U 132 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 36 removed outlier: 3.502A pdb=" N ARG V 33 " --> pdb=" O VAL V 29 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS V 34 " --> pdb=" O ALA V 30 " (cutoff:3.500A) Proline residue: V 36 - end of helix Processing helix chain 'V' and resid 116 through 121 removed outlier: 3.716A pdb=" N VAL V 120 " --> pdb=" O LEU V 116 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LYS V 121 " --> pdb=" O HIS V 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 116 through 121' Processing helix chain 'V' and resid 178 through 184 Processing helix chain 'V' and resid 193 through 203 removed outlier: 3.790A pdb=" N GLU V 200 " --> pdb=" O GLU V 196 " (cutoff:3.500A) Processing helix chain 'W' and resid 110 through 120 removed outlier: 4.162A pdb=" N ARG W 119 " --> pdb=" O ASP W 115 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU W 120 " --> pdb=" O LEU W 116 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 19 removed outlier: 3.811A pdb=" N TRP X 11 " --> pdb=" O PRO X 7 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU X 16 " --> pdb=" O LYS X 12 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG X 17 " --> pdb=" O ARG X 13 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLY X 19 " --> pdb=" O GLN X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 25 Proline residue: X 25 - end of helix Processing helix chain 'X' and resid 26 through 34 removed outlier: 4.073A pdb=" N SER X 31 " --> pdb=" O HIS X 27 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU X 32 " --> pdb=" O TYR X 28 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU X 33 " --> pdb=" O LEU X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 79 removed outlier: 4.303A pdb=" N GLN X 76 " --> pdb=" O PRO X 72 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG X 77 " --> pdb=" O PRO X 73 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU X 79 " --> pdb=" O SER X 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 72 through 79' Processing helix chain 'X' and resid 128 through 139 removed outlier: 3.597A pdb=" N ASP X 136 " --> pdb=" O LEU X 132 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU X 137 " --> pdb=" O ASP X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 148 removed outlier: 3.511A pdb=" N THR X 148 " --> pdb=" O TYR X 144 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 154 Processing helix chain 'X' and resid 155 through 172 Processing helix chain 'X' and resid 180 through 192 removed outlier: 3.682A pdb=" N ARG X 184 " --> pdb=" O ASP X 180 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA X 185 " --> pdb=" O PRO X 181 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA X 186 " --> pdb=" O GLU X 182 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 204 removed outlier: 4.322A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL X 204 " --> pdb=" O GLU X 200 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 220 Processing helix chain 'X' and resid 225 through 244 removed outlier: 3.624A pdb=" N ALA X 232 " --> pdb=" O LYS X 228 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN X 236 " --> pdb=" O ALA X 232 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU X 243 " --> pdb=" O GLN X 239 " (cutoff:3.500A) Processing helix chain 'Y' and resid 64 through 69 removed outlier: 4.456A pdb=" N PHE Y 68 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP Y 69 " --> pdb=" O GLU Y 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 64 through 69' Processing helix chain 'Y' and resid 70 through 75 removed outlier: 3.968A pdb=" N TRP Y 74 " --> pdb=" O ASP Y 70 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLY Y 75 " --> pdb=" O PRO Y 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 70 through 75' Processing helix chain 'Y' and resid 86 through 94 removed outlier: 3.610A pdb=" N LEU Y 90 " --> pdb=" O THR Y 86 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS Y 93 " --> pdb=" O GLN Y 89 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 123 removed outlier: 3.791A pdb=" N TYR Y 103 " --> pdb=" O HIS Y 99 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL Y 104 " --> pdb=" O LYS Y 100 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS Y 107 " --> pdb=" O TYR Y 103 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET Y 111 " --> pdb=" O LYS Y 107 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 158 removed outlier: 4.458A pdb=" N LEU Y 132 " --> pdb=" O SER Y 128 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL Y 135 " --> pdb=" O ARG Y 131 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP Y 143 " --> pdb=" O MET Y 139 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 198 removed outlier: 3.843A pdb=" N ARG Y 196 " --> pdb=" O LYS Y 192 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS Y 197 " --> pdb=" O ARG Y 193 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ARG Y 198 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 202 through 238 removed outlier: 4.369A pdb=" N ASP Y 206 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 48 removed outlier: 4.260A pdb=" N PHE Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA Z 48 " --> pdb=" O LYS Z 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 48' Processing helix chain 'Z' and resid 49 through 57 removed outlier: 3.833A pdb=" N GLU Z 54 " --> pdb=" O PRO Z 50 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY Z 57 " --> pdb=" O HIS Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 90 removed outlier: 4.066A pdb=" N ILE Z 85 " --> pdb=" O TRP Z 81 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS Z 87 " --> pdb=" O LYS Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 114 removed outlier: 3.758A pdb=" N ALA Z 108 " --> pdb=" O PRO Z 104 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL Z 112 " --> pdb=" O ALA Z 108 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL Z 113 " --> pdb=" O LYS Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 135 removed outlier: 5.612A pdb=" N SER Z 135 " --> pdb=" O GLU Z 131 " (cutoff:3.500A) Processing helix chain '0' and resid 86 through 95 removed outlier: 3.599A pdb=" N CYS 0 92 " --> pdb=" O GLU 0 88 " (cutoff:3.500A) Processing helix chain '0' and resid 124 through 146 removed outlier: 3.648A pdb=" N VAL 0 130 " --> pdb=" O CYS 0 126 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA 0 135 " --> pdb=" O CYS 0 131 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU 0 136 " --> pdb=" O LYS 0 132 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS 0 143 " --> pdb=" O ARG 0 139 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 64 Processing helix chain '2' and resid 65 through 72 removed outlier: 4.248A pdb=" N THR 2 72 " --> pdb=" O ARG 2 68 " (cutoff:3.500A) Processing helix chain '2' and resid 73 through 86 removed outlier: 3.894A pdb=" N GLN 2 77 " --> pdb=" O PRO 2 73 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL 2 78 " --> pdb=" O ALA 2 74 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 114 removed outlier: 3.942A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP 3 112 " --> pdb=" O LYS 3 108 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG 3 113 " --> pdb=" O ALA 3 109 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 137 removed outlier: 4.105A pdb=" N LYS 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N THR 3 137 " --> pdb=" O LEU 3 133 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 132 through 137' Processing helix chain '3' and resid 138 through 146 removed outlier: 4.663A pdb=" N GLU 3 146 " --> pdb=" O LYS 3 142 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 5.287A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 182 removed outlier: 4.061A pdb=" N HIS 3 181 " --> pdb=" O TYR 3 177 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASP 3 182 " --> pdb=" O GLN 3 178 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 177 through 182' Processing helix chain '5' and resid 47 through 52 removed outlier: 4.360A pdb=" N GLU 5 51 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE 5 52 " --> pdb=" O ARG 5 48 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 47 through 52' Processing helix chain '5' and resid 116 through 125 Processing helix chain '5' and resid 133 through 142 removed outlier: 3.553A pdb=" N SER 5 138 " --> pdb=" O GLU 5 134 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP 5 141 " --> pdb=" O LEU 5 137 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP 5 142 " --> pdb=" O SER 5 138 " (cutoff:3.500A) Processing helix chain '5' and resid 149 through 163 removed outlier: 3.625A pdb=" N VAL 5 154 " --> pdb=" O GLN 5 150 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU 5 155 " --> pdb=" O ASP 5 151 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN 5 156 " --> pdb=" O GLU 5 152 " (cutoff:3.500A) Processing helix chain '5' and resid 172 through 196 Proline residue: 5 178 - end of helix removed outlier: 3.566A pdb=" N VAL 5 181 " --> pdb=" O CYS 5 177 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU 5 184 " --> pdb=" O ILE 5 180 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU 5 187 " --> pdb=" O ASN 5 183 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LYS 5 194 " --> pdb=" O SER 5 190 " (cutoff:3.500A) Proline residue: 5 196 - end of helix Processing helix chain '5' and resid 241 through 252 removed outlier: 3.534A pdb=" N GLU 5 246 " --> pdb=" O ARG 5 242 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA 5 247 " --> pdb=" O GLU 5 243 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR 5 248 " --> pdb=" O GLU 5 244 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS 5 251 " --> pdb=" O ALA 5 247 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL 5 252 " --> pdb=" O THR 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 304 removed outlier: 5.554A pdb=" N LEU 5 304 " --> pdb=" O ARG 5 300 " (cutoff:3.500A) Processing helix chain '5' and resid 305 through 329 removed outlier: 3.727A pdb=" N ARG 5 310 " --> pdb=" O PRO 5 306 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA 5 311 " --> pdb=" O ASP 5 307 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU 5 327 " --> pdb=" O ALA 5 323 " (cutoff:3.500A) Processing helix chain '5' and resid 407 through 420 removed outlier: 4.652A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE 5 414 " --> pdb=" O THR 5 410 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 49 removed outlier: 4.615A pdb=" N LEU 6 48 " --> pdb=" O ASN 6 44 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU 6 49 " --> pdb=" O LEU 6 45 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 44 through 49' Processing helix chain '6' and resid 53 through 68 removed outlier: 4.030A pdb=" N TYR 6 57 " --> pdb=" O SER 6 53 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG 6 60 " --> pdb=" O ARG 6 56 " (cutoff:3.500A) Proline residue: 6 68 - end of helix Processing helix chain '6' and resid 73 through 78 removed outlier: 4.093A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 99 through 116 removed outlier: 3.540A pdb=" N ALA 6 115 " --> pdb=" O GLN 6 111 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN 6 116 " --> pdb=" O GLU 6 112 " (cutoff:3.500A) Processing helix chain '6' and resid 117 through 126 removed outlier: 3.644A pdb=" N ARG 6 124 " --> pdb=" O GLU 6 120 " (cutoff:3.500A) Processing helix chain '6' and resid 131 through 143 removed outlier: 3.813A pdb=" N VAL 6 135 " --> pdb=" O PRO 6 131 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG 6 141 " --> pdb=" O ALA 6 137 " (cutoff:3.500A) Processing helix chain '6' and resid 144 through 156 Processing helix chain '6' and resid 194 through 199 Processing helix chain '6' and resid 292 through 298 removed outlier: 6.552A pdb=" N PHE 6 298 " --> pdb=" O ALA 6 294 " (cutoff:3.500A) Processing helix chain '6' and resid 299 through 308 removed outlier: 4.029A pdb=" N LYS 6 306 " --> pdb=" O ASP 6 302 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS 6 307 " --> pdb=" O PHE 6 303 " (cutoff:3.500A) Processing helix chain '6' and resid 324 through 333 removed outlier: 4.214A pdb=" N THR 6 328 " --> pdb=" O ASP 6 324 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR 6 329 " --> pdb=" O ASP 6 325 " (cutoff:3.500A) Processing helix chain '6' and resid 364 through 371 removed outlier: 3.916A pdb=" N ARG 6 368 " --> pdb=" O ARG 6 364 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG 6 370 " --> pdb=" O LEU 6 366 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASP 6 371 " --> pdb=" O ASP 6 367 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 364 through 371' Processing helix chain '6' and resid 157 through 163 removed outlier: 4.307A pdb=" N PHE 6 162 " --> pdb=" O LEU 6 157 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 59 removed outlier: 3.510A pdb=" N THR 7 41 " --> pdb=" O PRO 7 37 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP 7 46 " --> pdb=" O GLU 7 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU 7 47 " --> pdb=" O MET 7 43 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU 7 58 " --> pdb=" O ARG 7 54 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR 7 59 " --> pdb=" O GLN 7 55 " (cutoff:3.500A) Processing helix chain '7' and resid 87 through 96 removed outlier: 3.520A pdb=" N HIS 7 94 " --> pdb=" O SER 7 90 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU 7 95 " --> pdb=" O CYS 7 91 " (cutoff:3.500A) Processing helix chain '7' and resid 97 through 102 Processing helix chain '7' and resid 135 through 158 removed outlier: 3.543A pdb=" N ALA 7 147 " --> pdb=" O TRP 7 143 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL 7 153 " --> pdb=" O MET 7 149 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG 7 156 " --> pdb=" O CYS 7 152 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 195 through 213 removed outlier: 3.602A pdb=" N LEU 7 199 " --> pdb=" O THR 7 195 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER 7 201 " --> pdb=" O GLU 7 197 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP 7 205 " --> pdb=" O SER 7 201 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE 7 210 " --> pdb=" O ALA 7 206 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS 7 212 " --> pdb=" O ALA 7 208 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP 7 213 " --> pdb=" O LEU 7 209 " (cutoff:3.500A) Processing helix chain '7' and resid 222 through 231 removed outlier: 3.530A pdb=" N LEU 7 227 " --> pdb=" O ALA 7 223 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU 7 228 " --> pdb=" O LYS 7 224 " (cutoff:3.500A) Processing helix chain '7' and resid 233 through 248 removed outlier: 3.554A pdb=" N PHE 7 239 " --> pdb=" O TYR 7 235 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER 7 245 " --> pdb=" O GLU 7 241 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN 7 247 " --> pdb=" O LYS 7 243 " (cutoff:3.500A) Proline residue: 7 248 - end of helix Processing helix chain '7' and resid 309 through 322 removed outlier: 3.566A pdb=" N LYS 7 315 " --> pdb=" O THR 7 311 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER 7 320 " --> pdb=" O LEU 7 316 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG 7 321 " --> pdb=" O LEU 7 317 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LYS 7 322 " --> pdb=" O GLU 7 318 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 3.927A pdb=" N ILE 7 274 " --> pdb=" O ARG 7 271 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS 7 275 " --> pdb=" O THR 7 272 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 271 through 276' Processing helix chain '8' and resid 107 through 154 removed outlier: 3.531A pdb=" N LYS 8 119 " --> pdb=" O ALA 8 115 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN 8 126 " --> pdb=" O SER 8 122 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET 8 139 " --> pdb=" O THR 8 135 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN 8 151 " --> pdb=" O LEU 8 147 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER 8 154 " --> pdb=" O LEU 8 150 " (cutoff:3.500A) Processing helix chain '8' and resid 155 through 164 removed outlier: 4.464A pdb=" N ALA 8 159 " --> pdb=" O PRO 8 155 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU 8 160 " --> pdb=" O LYS 8 156 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE 8 162 " --> pdb=" O HIS 8 158 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LYS 8 163 " --> pdb=" O ALA 8 159 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ARG 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain '8' and resid 167 through 172 removed outlier: 5.053A pdb=" N PHE 8 171 " --> pdb=" O ASN 8 167 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU 8 172 " --> pdb=" O LEU 8 168 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 167 through 172' Processing helix chain '9' and resid 27 through 35 removed outlier: 3.555A pdb=" N GLY 9 32 " --> pdb=" O ARG 9 28 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG 9 33 " --> pdb=" O SER 9 29 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS 9 34 " --> pdb=" O PHE 9 30 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLY 9 35 " --> pdb=" O ARG 9 31 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 58 removed outlier: 3.875A pdb=" N VAL 9 57 " --> pdb=" O ILE 9 53 " (cutoff:3.500A) Proline residue: 9 58 - end of helix No H-bonds generated for 'chain '9' and resid 53 through 58' Processing helix chain '9' and resid 87 through 95 Processing helix chain '9' and resid 96 through 106 removed outlier: 3.709A pdb=" N ASP 9 103 " --> pdb=" O ALA 9 99 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASP 9 106 " --> pdb=" O LYS 9 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 73 removed outlier: 3.991A pdb=" N THR a 72 " --> pdb=" O PRO a 68 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS a 73 " --> pdb=" O TYR a 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 68 through 73' Processing helix chain 'a' and resid 104 through 117 Processing helix chain 'a' and resid 127 through 134 removed outlier: 3.824A pdb=" N LYS a 134 " --> pdb=" O HIS a 130 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 21 removed outlier: 4.534A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG b 21 " --> pdb=" O ASN b 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 16 through 21' Processing helix chain 'b' and resid 37 through 49 removed outlier: 3.766A pdb=" N ARG b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA b 43 " --> pdb=" O SER b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 59 removed outlier: 3.517A pdb=" N ARG b 56 " --> pdb=" O ILE b 52 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN b 58 " --> pdb=" O PHE b 54 " (cutoff:3.500A) Proline residue: b 59 - end of helix Processing helix chain 'b' and resid 93 through 108 removed outlier: 3.724A pdb=" N THR b 99 " --> pdb=" O GLU b 95 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN b 107 " --> pdb=" O LYS b 103 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER b 108 " --> pdb=" O LEU b 104 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 53 removed outlier: 5.254A pdb=" N ALA c 38 " --> pdb=" O GLY c 34 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG c 47 " --> pdb=" O LYS c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 59 through 64 removed outlier: 4.158A pdb=" N LYS c 63 " --> pdb=" O ARG c 59 " (cutoff:3.500A) Proline residue: c 64 - end of helix No H-bonds generated for 'chain 'c' and resid 59 through 64' Processing helix chain 'c' and resid 67 through 80 removed outlier: 3.791A pdb=" N ILE c 72 " --> pdb=" O TYR c 68 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN c 73 " --> pdb=" O HIS c 69 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU c 79 " --> pdb=" O PHE c 75 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN c 80 " --> pdb=" O GLY c 76 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 94 removed outlier: 3.639A pdb=" N ALA c 91 " --> pdb=" O LEU c 87 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE c 92 " --> pdb=" O LEU c 88 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASN c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 107 removed outlier: 3.501A pdb=" N LYS c 99 " --> pdb=" O SER c 95 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS c 104 " --> pdb=" O SER c 100 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN c 106 " --> pdb=" O GLU c 102 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN c 107 " --> pdb=" O ALA c 103 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 145 removed outlier: 3.580A pdb=" N ASP c 143 " --> pdb=" O GLN c 139 " (cutoff:3.500A) Processing helix chain 'c' and resid 149 through 162 removed outlier: 3.664A pdb=" N PHE c 159 " --> pdb=" O ASN c 155 " (cutoff:3.500A) Processing helix chain 'c' and resid 163 through 174 removed outlier: 3.567A pdb=" N CYS c 167 " --> pdb=" O GLU c 163 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS c 168 " --> pdb=" O GLU c 164 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG c 171 " --> pdb=" O CYS c 167 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN c 172 " --> pdb=" O HIS c 168 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA c 174 " --> pdb=" O ALA c 170 " (cutoff:3.500A) Processing helix chain 'c' and resid 187 through 206 removed outlier: 3.539A pdb=" N GLN c 192 " --> pdb=" O PRO c 188 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN c 193 " --> pdb=" O ALA c 189 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN c 204 " --> pdb=" O GLY c 200 " (cutoff:3.500A) Processing helix chain 'c' and resid 207 through 224 removed outlier: 3.510A pdb=" N THR c 211 " --> pdb=" O GLY c 207 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU c 213 " --> pdb=" O GLU c 209 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE c 218 " --> pdb=" O PHE c 214 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE c 220 " --> pdb=" O ARG c 216 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN c 222 " --> pdb=" O PHE c 218 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N MET c 223 " --> pdb=" O LEU c 219 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR c 224 " --> pdb=" O ILE c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 removed outlier: 3.607A pdb=" N MET c 231 " --> pdb=" O GLU c 227 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS c 233 " --> pdb=" O PHE c 229 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 249 removed outlier: 3.506A pdb=" N VAL c 242 " --> pdb=" O MET c 238 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU c 243 " --> pdb=" O GLY c 239 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN c 249 " --> pdb=" O LEU c 245 " (cutoff:3.500A) Processing helix chain 'c' and resid 288 through 306 removed outlier: 3.791A pdb=" N ARG c 298 " --> pdb=" O GLU c 294 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 64 removed outlier: 3.565A pdb=" N PHE d 56 " --> pdb=" O THR d 52 " (cutoff:3.500A) Processing helix chain 'd' and resid 118 through 130 removed outlier: 3.834A pdb=" N ILE d 122 " --> pdb=" O SER d 118 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG d 123 " --> pdb=" O GLN d 119 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 155 removed outlier: 3.688A pdb=" N PHE d 137 " --> pdb=" O LYS d 133 " (cutoff:3.500A) Proline residue: d 138 - end of helix removed outlier: 3.572A pdb=" N ASP d 143 " --> pdb=" O GLU d 139 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU d 152 " --> pdb=" O ALA d 148 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN d 153 " --> pdb=" O HIS d 149 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 164 removed outlier: 4.293A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU d 163 " --> pdb=" O ARG d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 177 Proline residue: d 170 - end of helix removed outlier: 3.633A pdb=" N TRP d 174 " --> pdb=" O PRO d 170 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP d 175 " --> pdb=" O ASP d 171 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE d 176 " --> pdb=" O MET d 172 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 82 removed outlier: 3.869A pdb=" N GLU e 69 " --> pdb=" O PRO e 65 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN e 76 " --> pdb=" O SER e 72 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU e 78 " --> pdb=" O LEU e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 104 removed outlier: 5.155A pdb=" N GLU e 94 " --> pdb=" O ARG e 90 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN e 95 " --> pdb=" O ALA e 91 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN e 96 " --> pdb=" O LEU e 92 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG e 97 " --> pdb=" O ASP e 93 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS e 102 " --> pdb=" O LEU e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 116 through 132 removed outlier: 4.718A pdb=" N LEU e 120 " --> pdb=" O LEU e 116 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET e 123 " --> pdb=" O ASP e 119 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP e 124 " --> pdb=" O LEU e 120 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN e 126 " --> pdb=" O ASP e 122 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS e 127 " --> pdb=" O MET e 123 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE e 128 " --> pdb=" O TRP e 124 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 137 through 143 removed outlier: 5.583A pdb=" N ASP e 141 " --> pdb=" O ILE e 137 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU e 142 " --> pdb=" O THR e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 183 through 194 removed outlier: 4.068A pdb=" N LEU e 192 " --> pdb=" O ALA e 188 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ALA e 193 " --> pdb=" O GLU e 189 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR e 194 " --> pdb=" O ARG e 190 " (cutoff:3.500A) Processing helix chain 'e' and resid 256 through 264 removed outlier: 5.862A pdb=" N LEU e 260 " --> pdb=" O THR e 256 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY e 261 " --> pdb=" O LYS e 257 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU e 264 " --> pdb=" O LEU e 260 " (cutoff:3.500A) Processing helix chain 'e' and resid 267 through 277 removed outlier: 4.714A pdb=" N GLN e 271 " --> pdb=" O LYS e 267 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL e 272 " --> pdb=" O TYR e 268 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ARG e 273 " --> pdb=" O LEU e 269 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG e 274 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N PHE e 275 " --> pdb=" O GLN e 271 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL e 276 " --> pdb=" O VAL e 272 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N SER e 277 " --> pdb=" O ARG e 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 267 through 277' Processing helix chain 'f' and resid 59 through 64 removed outlier: 3.921A pdb=" N ILE f 63 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS f 64 " --> pdb=" O LYS f 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 59 through 64' Processing helix chain 'f' and resid 99 through 118 removed outlier: 3.619A pdb=" N TYR f 106 " --> pdb=" O LEU f 102 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR f 109 " --> pdb=" O SER f 105 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL f 110 " --> pdb=" O TYR f 106 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS f 111 " --> pdb=" O ALA f 107 " (cutoff:3.500A) Processing helix chain 'f' and resid 163 through 178 removed outlier: 4.428A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE f 169 " --> pdb=" O THR f 165 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE f 174 " --> pdb=" O PHE f 170 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU f 178 " --> pdb=" O ILE f 174 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 53 removed outlier: 4.603A pdb=" N VAL g 48 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG g 50 " --> pdb=" O GLN g 46 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU g 52 " --> pdb=" O VAL g 48 " (cutoff:3.500A) Proline residue: g 53 - end of helix Processing helix chain 'g' and resid 116 through 132 removed outlier: 3.515A pdb=" N LEU g 120 " --> pdb=" O ASP g 116 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER g 129 " --> pdb=" O GLU g 125 " (cutoff:3.500A) Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 153 through 165 removed outlier: 3.598A pdb=" N TRP g 160 " --> pdb=" O GLU g 156 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY g 165 " --> pdb=" O LEU g 161 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 78 Processing helix chain 'h' and resid 93 through 108 removed outlier: 3.553A pdb=" N HIS h 103 " --> pdb=" O ASN h 99 " (cutoff:3.500A) Processing helix chain 'h' and resid 113 through 118 removed outlier: 4.647A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 132 removed outlier: 3.626A pdb=" N VAL h 126 " --> pdb=" O ARG h 122 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN h 131 " --> pdb=" O LEU h 127 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL h 132 " --> pdb=" O ASP h 128 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 147 removed outlier: 3.549A pdb=" N ALA h 145 " --> pdb=" O ASP h 141 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER h 146 " --> pdb=" O GLU h 142 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN h 147 " --> pdb=" O LEU h 143 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 54 removed outlier: 3.753A pdb=" N PHE i 54 " --> pdb=" O LYS i 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 59 through 64 Processing helix chain 'i' and resid 69 through 74 removed outlier: 4.250A pdb=" N LEU i 73 " --> pdb=" O HIS i 69 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE i 74 " --> pdb=" O PRO i 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 69 through 74' Processing helix chain 'i' and resid 86 through 98 Processing helix chain 'i' and resid 103 through 123 removed outlier: 3.581A pdb=" N HIS i 108 " --> pdb=" O ALA i 104 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN i 109 " --> pdb=" O ASP i 105 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS i 119 " --> pdb=" O ARG i 115 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 32 removed outlier: 4.367A pdb=" N ARG j 28 " --> pdb=" O GLY j 24 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN j 30 " --> pdb=" O GLN j 26 " (cutoff:3.500A) Processing helix chain 'j' and resid 60 through 107 removed outlier: 3.571A pdb=" N TRP j 91 " --> pdb=" O GLY j 87 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN j 96 " --> pdb=" O GLN j 92 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN j 99 " --> pdb=" O GLN j 95 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU j 101 " --> pdb=" O LYS j 97 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN j 102 " --> pdb=" O LEU j 98 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN j 105 " --> pdb=" O GLU j 101 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU j 106 " --> pdb=" O GLN j 102 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASN j 107 " --> pdb=" O ARG j 103 " (cutoff:3.500A) Processing helix chain 'k' and resid 27 through 39 removed outlier: 3.539A pdb=" N ARG k 31 " --> pdb=" O VAL k 27 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER k 39 " --> pdb=" O GLN k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 40 through 47 removed outlier: 3.900A pdb=" N SER k 44 " --> pdb=" O GLU k 40 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N THR k 45 " --> pdb=" O LYS k 41 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 96 removed outlier: 3.605A pdb=" N HIS k 93 " --> pdb=" O ALA k 89 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG k 95 " --> pdb=" O ALA k 91 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 135 removed outlier: 4.147A pdb=" N TRP l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASN l 135 " --> pdb=" O ARG l 131 " (cutoff:3.500A) Processing helix chain 'o' and resid 28 through 52 removed outlier: 3.788A pdb=" N ILE o 41 " --> pdb=" O ARG o 37 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER o 50 " --> pdb=" O HIS o 46 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N MET o 51 " --> pdb=" O TYR o 47 " (cutoff:3.500A) Proline residue: o 52 - end of helix Processing helix chain 'o' and resid 55 through 60 removed outlier: 4.083A pdb=" N ARG o 60 " --> pdb=" O ARG o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 81 removed outlier: 3.663A pdb=" N SER o 80 " --> pdb=" O ALA o 76 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 100 removed outlier: 3.505A pdb=" N GLN o 91 " --> pdb=" O PHE o 87 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP o 93 " --> pdb=" O ALA o 89 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS o 99 " --> pdb=" O LEU o 95 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LYS o 100 " --> pdb=" O ASN o 96 " (cutoff:3.500A) Processing helix chain 'p' and resid 44 through 50 removed outlier: 3.556A pdb=" N TYR p 49 " --> pdb=" O LEU p 45 " (cutoff:3.500A) Proline residue: p 50 - end of helix Processing helix chain 'p' and resid 72 through 77 removed outlier: 3.887A pdb=" N LEU p 76 " --> pdb=" O PRO p 72 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR p 77 " --> pdb=" O LEU p 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 72 through 77' Processing helix chain 'p' and resid 112 through 124 removed outlier: 3.600A pdb=" N GLN p 117 " --> pdb=" O GLU p 113 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS p 124 " --> pdb=" O ALA p 120 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 163 removed outlier: 3.849A pdb=" N GLU p 160 " --> pdb=" O ASP p 156 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN p 163 " --> pdb=" O THR p 159 " (cutoff:3.500A) Processing helix chain 'p' and resid 174 through 190 removed outlier: 4.665A pdb=" N ILE p 178 " --> pdb=" O LYS p 174 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE p 180 " --> pdb=" O HIS p 176 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU p 188 " --> pdb=" O ASN p 184 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG p 189 " --> pdb=" O ARG p 185 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN p 190 " --> pdb=" O GLU p 186 " (cutoff:3.500A) Processing helix chain 'q' and resid 48 through 53 removed outlier: 3.814A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 48 through 53' Processing helix chain 'q' and resid 54 through 65 removed outlier: 3.582A pdb=" N ARG q 63 " --> pdb=" O LYS q 59 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR q 64 " --> pdb=" O GLN q 60 " (cutoff:3.500A) Processing helix chain 'q' and resid 78 through 92 removed outlier: 3.505A pdb=" N GLU q 84 " --> pdb=" O GLU q 80 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU q 91 " --> pdb=" O ALA q 87 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP q 92 " --> pdb=" O GLU q 88 " (cutoff:3.500A) Processing helix chain 'q' and resid 95 through 152 removed outlier: 3.678A pdb=" N HIS q 120 " --> pdb=" O GLU q 116 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS q 127 " --> pdb=" O GLU q 123 " (cutoff:3.500A) Proline residue: q 129 - end of helix removed outlier: 3.631A pdb=" N GLN q 138 " --> pdb=" O ASN q 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN q 147 " --> pdb=" O TRP q 143 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP q 149 " --> pdb=" O LYS q 145 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU q 151 " --> pdb=" O GLN q 147 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG q 152 " --> pdb=" O ALA q 148 " (cutoff:3.500A) Processing helix chain 'q' and resid 71 through 76 removed outlier: 3.551A pdb=" N SER q 74 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU q 75 " --> pdb=" O PRO q 72 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TRP q 76 " --> pdb=" O GLY q 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 71 through 76' Processing helix chain 'r' and resid 70 through 76 removed outlier: 3.567A pdb=" N TRP r 75 " --> pdb=" O PRO r 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 removed outlier: 4.443A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG r 94 " --> pdb=" O SER r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 106 Processing helix chain 'r' and resid 108 through 126 removed outlier: 3.892A pdb=" N ARG r 113 " --> pdb=" O GLN r 109 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS r 120 " --> pdb=" O GLU r 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA r 125 " --> pdb=" O MET r 121 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY r 126 " --> pdb=" O ALA r 122 " (cutoff:3.500A) Processing helix chain 's' and resid 55 through 73 removed outlier: 3.617A pdb=" N ARG s 59 " --> pdb=" O SER s 55 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR s 69 " --> pdb=" O ARG s 65 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL s 70 " --> pdb=" O TRP s 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS s 71 " --> pdb=" O GLN s 67 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 85 Processing helix chain 's' and resid 101 through 111 removed outlier: 3.738A pdb=" N TRP s 105 " --> pdb=" O ASN s 101 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR s 108 " --> pdb=" O ARG s 104 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR s 110 " --> pdb=" O TYR s 106 " (cutoff:3.500A) Processing helix chain 's' and resid 140 through 155 removed outlier: 3.531A pdb=" N LEU s 150 " --> pdb=" O ALA s 146 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU s 153 " --> pdb=" O CYS s 149 " (cutoff:3.500A) Processing helix chain 's' and resid 164 through 169 removed outlier: 4.153A pdb=" N GLU s 168 " --> pdb=" O HIS s 164 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER s 169 " --> pdb=" O ARG s 165 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 164 through 169' Processing helix chain 's' and resid 171 through 193 Proline residue: s 175 - end of helix removed outlier: 3.881A pdb=" N GLY s 186 " --> pdb=" O SER s 182 " (cutoff:3.500A) Proline residue: s 190 - end of helix Proline residue: s 193 - end of helix Processing helix chain 's' and resid 267 through 272 removed outlier: 4.464A pdb=" N LEU s 271 " --> pdb=" O LYS s 267 " (cutoff:3.500A) Proline residue: s 272 - end of helix No H-bonds generated for 'chain 's' and resid 267 through 272' Processing helix chain 's' and resid 307 through 315 removed outlier: 4.525A pdb=" N ASN s 315 " --> pdb=" O LEU s 311 " (cutoff:3.500A) Processing helix chain 's' and resid 318 through 344 removed outlier: 4.320A pdb=" N VAL s 322 " --> pdb=" O ASP s 318 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE s 324 " --> pdb=" O ILE s 320 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA s 328 " --> pdb=" O PHE s 324 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY s 344 " --> pdb=" O ALA s 340 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 385 removed outlier: 3.751A pdb=" N GLN s 385 " --> pdb=" O THR s 381 " (cutoff:3.500A) Processing helix chain 's' and resid 414 through 427 removed outlier: 4.170A pdb=" N LEU s 418 " --> pdb=" O ASN s 414 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN s 427 " --> pdb=" O HIS s 423 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 105 removed outlier: 3.820A pdb=" N SER u 99 " --> pdb=" O ASP u 95 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU u 101 " --> pdb=" O MET u 97 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG u 102 " --> pdb=" O VAL u 98 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN u 103 " --> pdb=" O SER u 99 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU u 104 " --> pdb=" O LEU u 100 " (cutoff:3.500A) Processing helix chain 'u' and resid 131 through 149 removed outlier: 3.581A pdb=" N VAL u 143 " --> pdb=" O ALA u 139 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS u 144 " --> pdb=" O PHE u 140 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU u 149 " --> pdb=" O MET u 145 " (cutoff:3.500A) Processing helix chain 'u' and resid 181 through 189 removed outlier: 3.632A pdb=" N GLU u 186 " --> pdb=" O PRO u 182 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE u 187 " --> pdb=" O GLU u 183 " (cutoff:3.500A) Processing helix chain 'u' and resid 190 through 196 removed outlier: 3.783A pdb=" N TRP u 194 " --> pdb=" O LEU u 190 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR u 195 " --> pdb=" O GLU u 191 " (cutoff:3.500A) Processing helix chain 'v' and resid 5 through 24 removed outlier: 4.268A pdb=" N VAL v 9 " --> pdb=" O SER v 5 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU v 10 " --> pdb=" O ARG v 6 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA v 15 " --> pdb=" O SER v 11 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU v 17 " --> pdb=" O TYR v 13 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU v 23 " --> pdb=" O GLN v 19 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG v 24 " --> pdb=" O GLY v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 41 removed outlier: 3.764A pdb=" N ARG v 36 " --> pdb=" O PHE v 32 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG v 37 " --> pdb=" O ALA v 33 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS v 41 " --> pdb=" O ARG v 37 " (cutoff:3.500A) Processing helix chain 'v' and resid 47 through 64 removed outlier: 3.669A pdb=" N ARG v 51 " --> pdb=" O ASP v 47 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU v 52 " --> pdb=" O ALA v 48 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG v 53 " --> pdb=" O GLU v 49 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY v 58 " --> pdb=" O GLN v 54 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU v 59 " --> pdb=" O LEU v 55 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL v 60 " --> pdb=" O GLU v 56 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 90 removed outlier: 3.620A pdb=" N ILE w 79 " --> pdb=" O THR w 75 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN w 80 " --> pdb=" O LEU w 76 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL w 83 " --> pdb=" O ILE w 79 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR w 85 " --> pdb=" O ASP w 81 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS w 88 " --> pdb=" O LEU w 84 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR w 90 " --> pdb=" O VAL w 86 " (cutoff:3.500A) Processing helix chain 'w' and resid 113 through 126 removed outlier: 4.058A pdb=" N GLU w 117 " --> pdb=" O LEU w 113 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP w 124 " --> pdb=" O MET w 120 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU w 125 " --> pdb=" O ALA w 121 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 139 removed outlier: 5.322A pdb=" N LYS w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU w 138 " --> pdb=" O ASP w 134 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N MET w 139 " --> pdb=" O ALA w 135 " (cutoff:3.500A) Processing helix chain 'w' and resid 140 through 152 removed outlier: 3.650A pdb=" N ASP w 146 " --> pdb=" O GLN w 142 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA w 149 " --> pdb=" O VAL w 145 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP w 150 " --> pdb=" O ASP w 146 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS w 151 " --> pdb=" O TYR w 147 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS w 152 " --> pdb=" O ILE w 148 " (cutoff:3.500A) Processing helix chain 'w' and resid 103 through 109 removed outlier: 4.179A pdb=" N LEU w 108 " --> pdb=" O HIS w 103 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 15 removed outlier: 3.852A pdb=" N ARG n 8 " --> pdb=" O GLY n 4 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA n 9 " --> pdb=" O LYS n 5 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU n 10 " --> pdb=" O ARG n 6 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU n 11 " --> pdb=" O TYR n 7 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU n 12 " --> pdb=" O ARG n 8 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS n 13 " --> pdb=" O ALA n 9 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASP n 15 " --> pdb=" O LEU n 11 " (cutoff:3.500A) Processing helix chain 'n' and resid 21 through 34 removed outlier: 3.688A pdb=" N HIS n 27 " --> pdb=" O ASP n 23 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU n 28 " --> pdb=" O GLU n 24 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS n 30 " --> pdb=" O ALA n 26 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLU n 31 " --> pdb=" O HIS n 27 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU n 32 " --> pdb=" O LEU n 28 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA n 33 " --> pdb=" O VAL n 29 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N THR n 34 " --> pdb=" O LYS n 30 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 90 removed outlier: 4.581A pdb=" N LYS n 84 " --> pdb=" O GLY n 80 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU n 85 " --> pdb=" O GLU n 81 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU n 87 " --> pdb=" O ILE n 83 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU n 88 " --> pdb=" O LYS n 84 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA n 89 " --> pdb=" O GLU n 85 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY n 90 " --> pdb=" O ALA n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 99 through 106 removed outlier: 4.198A pdb=" N ILE n 103 " --> pdb=" O ILE n 99 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU n 104 " --> pdb=" O ILE n 100 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP n 105 " --> pdb=" O GLN n 101 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY n 106 " --> pdb=" O LYS n 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 99 through 106' Processing helix chain 'n' and resid 116 through 127 removed outlier: 3.654A pdb=" N MET n 120 " --> pdb=" O THR n 116 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLY n 121 " --> pdb=" O PRO n 117 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA n 122 " --> pdb=" O ASP n 118 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY n 124 " --> pdb=" O MET n 120 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER n 125 " --> pdb=" O GLY n 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS n 126 " --> pdb=" O ALA n 122 " (cutoff:3.500A) Processing helix chain 'n' and resid 128 through 135 Proline residue: n 133 - end of helix Processing helix chain 'n' and resid 148 through 159 removed outlier: 3.525A pdb=" N LYS n 157 " --> pdb=" O ILE n 153 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA n 158 " --> pdb=" O ARG n 154 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY n 159 " --> pdb=" O GLU n 155 " (cutoff:3.500A) Processing helix chain 'n' and resid 181 through 200 removed outlier: 3.586A pdb=" N ASN n 188 " --> pdb=" O LYS n 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 171 removed outlier: 3.818A pdb=" N LYS C 165 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N CYS C 170 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ARG C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 195 removed outlier: 3.774A pdb=" N VAL C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LYS C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'D' and resid 121 through 126 removed outlier: 4.500A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'D' and resid 128 through 131 Processing sheet with id= 3, first strand: chain 'D' and resid 214 through 217 removed outlier: 6.944A pdb=" N ILE D 225 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS D 293 " --> pdb=" O GLN D 233 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'E' and resid 98 through 101 Processing sheet with id= 5, first strand: chain 'E' and resid 105 through 111 removed outlier: 3.742A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ASN E 281 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 176 through 181 removed outlier: 6.402A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N CYS E 127 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR E 191 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 202 through 205 removed outlier: 4.428A pdb=" N GLN E 202 " --> pdb=" O VAL E 273 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'F' and resid 46 through 50 removed outlier: 4.440A pdb=" N VAL F 47 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG F 49 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY F 78 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 108 through 111 removed outlier: 5.725A pdb=" N ARG F 108 " --> pdb=" O TYR F 161 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 186 through 189 Processing sheet with id= 11, first strand: chain 'H' and resid 95 through 98 removed outlier: 4.424A pdb=" N ASP H 110 " --> pdb=" O LEU H 98 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'I' and resid 94 through 100 removed outlier: 4.597A pdb=" N ALA I 97 " --> pdb=" O LEU I 154 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'J' and resid 18 through 26 removed outlier: 3.594A pdb=" N ALA J 22 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL J 24 " --> pdb=" O LEU J 66 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ILE J 64 " --> pdb=" O ALA J 26 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY J 83 " --> pdb=" O PRO J 67 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS J 81 " --> pdb=" O LYS J 69 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU J 71 " --> pdb=" O GLU J 79 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU J 79 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'K' and resid 55 through 60 removed outlier: 3.689A pdb=" N GLU K 143 " --> pdb=" O TRP K 18 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP K 22 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'L' and resid 38 through 41 Processing sheet with id= 16, first strand: chain 'L' and resid 72 through 76 Processing sheet with id= 17, first strand: chain 'M' and resid 93 through 96 Processing sheet with id= 18, first strand: chain 'M' and resid 152 through 157 Processing sheet with id= 19, first strand: chain 'M' and resid 273 through 277 Processing sheet with id= 20, first strand: chain 'N' and resid 94 through 97 Processing sheet with id= 21, first strand: chain 'N' and resid 119 through 123 removed outlier: 6.152A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE N 87 " --> pdb=" O MET N 163 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA N 186 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'O' and resid 40 through 45 removed outlier: 7.358A pdb=" N GLU O 40 " --> pdb=" O TYR O 125 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE O 123 " --> pdb=" O ILE O 42 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE O 110 " --> pdb=" O MET O 120 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N TYR O 104 " --> pdb=" O LYS O 126 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'P' and resid 79 through 85 Processing sheet with id= 24, first strand: chain 'Q' and resid 129 through 135 removed outlier: 4.541A pdb=" N LYS Q 129 " --> pdb=" O ASP Q 123 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU Q 173 " --> pdb=" O THR Q 120 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Q' and resid 139 through 142 removed outlier: 3.735A pdb=" N GLN Q 139 " --> pdb=" O ILE Q 150 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER Q 141 " --> pdb=" O THR Q 148 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'S' and resid 96 through 100 Processing sheet with id= 27, first strand: chain 'S' and resid 112 through 117 removed outlier: 3.831A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL S 160 " --> pdb=" O GLU S 126 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLU S 126 " --> pdb=" O VAL S 160 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'S' and resid 162 through 166 removed outlier: 3.855A pdb=" N GLU S 162 " --> pdb=" O VAL S 192 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N THR S 188 " --> pdb=" O SER S 166 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'S' and resid 168 through 175 removed outlier: 4.126A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'T' and resid 71 through 78 removed outlier: 4.703A pdb=" N ALA T 71 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS T 177 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'T' and resid 152 through 159 No H-bonds generated for sheet with id= 31 Processing sheet with id= 32, first strand: chain 'U' and resid 26 through 29 removed outlier: 3.710A pdb=" N GLN U 27 " --> pdb=" O ARG U 43 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP U 38 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LYS U 88 " --> pdb=" O ASN U 77 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN U 77 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY U 75 " --> pdb=" O PRO U 90 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'V' and resid 62 through 65 No H-bonds generated for sheet with id= 33 Processing sheet with id= 34, first strand: chain 'V' and resid 78 through 81 removed outlier: 3.718A pdb=" N GLN V 78 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE V 80 " --> pdb=" O TRP V 85 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'V' and resid 92 through 97 removed outlier: 5.836A pdb=" N ASN V 92 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'V' and resid 132 through 135 removed outlier: 7.085A pdb=" N GLU V 132 " --> pdb=" O THR V 148 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'W' and resid 81 through 84 removed outlier: 4.773A pdb=" N CYS W 88 " --> pdb=" O GLY W 84 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'W' and resid 97 through 102 Processing sheet with id= 39, first strand: chain 'X' and resid 49 through 52 removed outlier: 5.439A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'X' and resid 85 through 92 removed outlier: 6.806A pdb=" N LYS X 99 " --> pdb=" O ALA X 92 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'Y' and resid 165 through 170 Processing sheet with id= 42, first strand: chain 'Z' and resid 97 through 101 removed outlier: 5.103A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '0' and resid 155 through 159 Processing sheet with id= 44, first strand: chain '1' and resid 16 through 22 removed outlier: 5.924A pdb=" N PHE 1 28 " --> pdb=" O SER 1 22 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '1' and resid 42 through 46 Processing sheet with id= 46, first strand: chain '3' and resid 122 through 125 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain '4' and resid 66 through 69 removed outlier: 7.008A pdb=" N TRP 4 88 " --> pdb=" O GLN 4 102 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '5' and resid 126 through 130 removed outlier: 3.643A pdb=" N PHE 5 354 " --> pdb=" O ASP 5 377 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL 5 351 " --> pdb=" O ASP 5 348 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '5' and resid 200 through 205 removed outlier: 9.297A pdb=" N ARG 5 200 " --> pdb=" O LYS 5 233 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '5' and resid 206 through 214 removed outlier: 4.598A pdb=" N SER 5 207 " --> pdb=" O GLY 5 226 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY 5 226 " --> pdb=" O SER 5 207 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE 5 209 " --> pdb=" O GLY 5 224 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU 5 219 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN 5 221 " --> pdb=" O TYR 5 105 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain '5' and resid 389 through 392 removed outlier: 7.739A pdb=" N LEU 5 389 " --> pdb=" O VAL 5 401 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL 5 401 " --> pdb=" O LEU 5 389 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU 5 399 " --> pdb=" O VAL 5 391 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain '6' and resid 184 through 187 removed outlier: 4.257A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA 6 176 " --> pdb=" O GLU 6 203 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain '6' and resid 190 through 193 removed outlier: 3.638A pdb=" N ASN 6 191 " --> pdb=" O PHE 6 318 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG 6 322 " --> pdb=" O VAL 6 193 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LYS 6 274 " --> pdb=" O PRO 6 313 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU 6 272 " --> pdb=" O GLY 6 315 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU 6 213 " --> pdb=" O GLN 6 275 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP 6 235 " --> pdb=" O LEU 6 218 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain '7' and resid 77 through 82 removed outlier: 4.359A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N CYS 7 123 " --> pdb=" O GLU 7 66 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE 7 127 " --> pdb=" O VAL 7 70 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain '7' and resid 163 through 167 removed outlier: 6.851A pdb=" N MET 7 163 " --> pdb=" O ASP 7 186 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP 7 182 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain '7' and resid 217 through 221 Processing sheet with id= 57, first strand: chain '7' and resid 281 through 286 removed outlier: 5.707A pdb=" N ILE 7 294 " --> pdb=" O LEU 7 286 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain '9' and resid 42 through 45 removed outlier: 3.690A pdb=" N ARG 9 49 " --> pdb=" O THR 9 45 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'a' and resid 45 through 51 Processing sheet with id= 60, first strand: chain 'b' and resid 61 through 68 removed outlier: 6.263A pdb=" N VAL b 33 " --> pdb=" O ASN b 66 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG b 68 " --> pdb=" O VAL b 33 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG b 74 " --> pdb=" O SER b 32 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER b 88 " --> pdb=" O PRO b 73 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL b 75 " --> pdb=" O GLU b 86 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU b 86 " --> pdb=" O VAL b 75 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA b 77 " --> pdb=" O VAL b 84 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL b 84 " --> pdb=" O ALA b 77 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N TYR b 79 " --> pdb=" O GLY b 82 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'c' and resid 254 through 257 Processing sheet with id= 62, first strand: chain 'c' and resid 269 through 274 removed outlier: 4.078A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'd' and resid 212 through 219 removed outlier: 3.573A pdb=" N VAL d 242 " --> pdb=" O THR d 218 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL d 247 " --> pdb=" O HIS d 262 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'e' and resid 174 through 178 removed outlier: 5.167A pdb=" N LEU e 47 " --> pdb=" O TRP e 178 " (cutoff:3.500A) removed outlier: 11.626A pdb=" N LEU e 51 " --> pdb=" O VAL e 161 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N VAL e 161 " --> pdb=" O LEU e 51 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU e 53 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU e 159 " --> pdb=" O LEU e 53 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU e 157 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL e 158 " --> pdb=" O VAL e 255 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL e 255 " --> pdb=" O VAL e 158 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG e 162 " --> pdb=" O HIS e 251 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N HIS e 251 " --> pdb=" O ARG e 162 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'e' and resid 201 through 204 removed outlier: 7.284A pdb=" N GLU e 201 " --> pdb=" O LEU e 239 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU e 227 " --> pdb=" O PHE e 217 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA e 229 " --> pdb=" O PHE e 215 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE e 215 " --> pdb=" O ALA e 229 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL e 231 " --> pdb=" O TYR e 213 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR e 213 " --> pdb=" O VAL e 231 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'f' and resid 78 through 81 removed outlier: 7.123A pdb=" N ARG f 78 " --> pdb=" O GLY f 89 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY f 89 " --> pdb=" O ARG f 78 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'f' and resid 123 through 127 removed outlier: 4.542A pdb=" N GLU f 123 " --> pdb=" O GLN f 158 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU f 154 " --> pdb=" O MET f 127 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS f 94 " --> pdb=" O SER f 185 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'g' and resid 95 through 101 removed outlier: 5.501A pdb=" N VAL g 137 " --> pdb=" O LYS g 150 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'k' and resid 49 through 56 removed outlier: 3.736A pdb=" N VAL k 16 " --> pdb=" O SER k 50 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE k 20 " --> pdb=" O ASP k 54 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N HIS k 72 " --> pdb=" O PHE k 68 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'm' and resid 53 through 57 Processing sheet with id= 71, first strand: chain 'p' and resid 78 through 82 removed outlier: 3.656A pdb=" N PHE p 103 " --> pdb=" O LEU p 133 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'r' and resid 35 through 41 removed outlier: 4.260A pdb=" N PHE r 35 " --> pdb=" O THR r 54 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 's' and resid 112 through 116 removed outlier: 6.591A pdb=" N ASN s 391 " --> pdb=" O ASN s 375 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN s 375 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N CYS s 393 " --> pdb=" O GLN s 373 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLN s 373 " --> pdb=" O CYS s 393 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY s 395 " --> pdb=" O CYS s 371 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N CYS s 371 " --> pdb=" O GLY s 395 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLN s 397 " --> pdb=" O PHE s 369 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N PHE s 369 " --> pdb=" O GLN s 397 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N LYS s 365 " --> pdb=" O LEU s 401 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR s 297 " --> pdb=" O ILE s 241 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN s 239 " --> pdb=" O PHE s 299 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 's' and resid 213 through 217 removed outlier: 4.790A pdb=" N GLY s 213 " --> pdb=" O LEU s 229 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU s 229 " --> pdb=" O GLY s 213 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG s 225 " --> pdb=" O ILE s 217 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N MET s 89 " --> pdb=" O ASP s 228 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ARG s 230 " --> pdb=" O MET s 89 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE s 274 " --> pdb=" O MET s 92 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 's' and resid 241 through 244 removed outlier: 6.612A pdb=" N ILE s 241 " --> pdb=" O HIS s 296 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'u' and resid 107 through 114 removed outlier: 3.787A pdb=" N ASP u 108 " --> pdb=" O SER u 128 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP u 122 " --> pdb=" O VAL u 114 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N MET u 175 " --> pdb=" O PHE u 172 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'n' and resid 41 through 46 removed outlier: 4.231A pdb=" N SER n 211 " --> pdb=" O LYS n 46 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL n 212 " --> pdb=" O ILE n 224 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'n' and resid 59 through 63 Processing sheet with id= 79, first strand: chain 'n' and resid 74 through 77 Processing sheet with id= 80, first strand: chain 'C' and resid 218 through 221 removed outlier: 3.571A pdb=" N TYR C 219 " --> pdb=" O MET C 235 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 233 " --> pdb=" O CYS C 221 " (cutoff:3.500A) 2210 hydrogen bonds defined for protein. 6552 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 930 hydrogen bonds 1582 hydrogen bond angles 0 basepair planarities 391 basepair parallelities 937 stacking parallelities Total time for adding SS restraints: 62.33 Time building geometry restraints manager: 38.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 13786 1.31 - 1.44: 39866 1.44 - 1.56: 54475 1.56 - 1.69: 3364 1.69 - 1.82: 464 Bond restraints: 111955 Sorted by residual: bond pdb=" C LYS i 68 " pdb=" N HIS i 69 " ideal model delta sigma weight residual 1.330 1.243 0.087 1.47e-02 4.63e+03 3.46e+01 bond pdb=" C LEU C 184 " pdb=" N ASN C 185 " ideal model delta sigma weight residual 1.328 1.251 0.077 1.45e-02 4.76e+03 2.80e+01 bond pdb=" C VAL T 58 " pdb=" N TYR T 59 " ideal model delta sigma weight residual 1.330 1.261 0.069 1.47e-02 4.63e+03 2.20e+01 bond pdb=" CA HIS H 88 " pdb=" C HIS H 88 " ideal model delta sigma weight residual 1.526 1.468 0.058 1.28e-02 6.10e+03 2.04e+01 bond pdb=" C GLU k 61 " pdb=" N PRO k 62 " ideal model delta sigma weight residual 1.328 1.377 -0.049 1.25e-02 6.40e+03 1.57e+01 ... (remaining 111950 not shown) Histogram of bond angle deviations from ideal: 68.22 - 82.33: 5 82.33 - 96.45: 2 96.45 - 110.56: 47896 110.56 - 124.68: 103527 124.68 - 138.80: 8055 Bond angle restraints: 159485 Sorted by residual: angle pdb=" CB 4HH w 112 " pdb=" OG 4HH w 112 " pdb=" P 4HH w 112 " ideal model delta sigma weight residual 119.19 71.20 47.99 3.00e+00 1.11e-01 2.56e+02 angle pdb=" OP1 C A2920 " pdb=" P C A2920 " pdb=" OP2 C A2920 " ideal model delta sigma weight residual 119.60 79.67 39.93 3.00e+00 1.11e-01 1.77e+02 angle pdb=" OG 4HH w 112 " pdb=" P 4HH w 112 " pdb=" O1P 4HH w 112 " ideal model delta sigma weight residual 106.46 68.22 38.24 3.00e+00 1.11e-01 1.62e+02 angle pdb=" OP2 C A2920 " pdb=" P C A2920 " pdb=" O5' C A2920 " ideal model delta sigma weight residual 108.00 73.93 34.07 3.00e+00 1.11e-01 1.29e+02 angle pdb=" O3' A A2919 " pdb=" P C A2920 " pdb=" OP1 C A2920 " ideal model delta sigma weight residual 108.00 76.44 31.56 3.00e+00 1.11e-01 1.11e+02 ... (remaining 159480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 64088 35.99 - 71.98: 4385 71.98 - 107.97: 582 107.97 - 143.96: 16 143.96 - 179.96: 39 Dihedral angle restraints: 69110 sinusoidal: 43939 harmonic: 25171 Sorted by residual: dihedral pdb=" CA GLN 8 186 " pdb=" C GLN 8 186 " pdb=" N PRO 8 187 " pdb=" CA PRO 8 187 " ideal model delta harmonic sigma weight residual 180.00 123.26 56.74 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" O4' C A2079 " pdb=" C1' C A2079 " pdb=" N1 C A2079 " pdb=" C2 C A2079 " ideal model delta sinusoidal sigma weight residual -160.00 19.58 -179.58 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A2493 " pdb=" C1' C A2493 " pdb=" N1 C A2493 " pdb=" C2 C A2493 " ideal model delta sinusoidal sigma weight residual -160.00 17.87 -177.87 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 69107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 16771 0.080 - 0.161: 1913 0.161 - 0.241: 144 0.241 - 0.322: 24 0.322 - 0.402: 10 Chirality restraints: 18862 Sorted by residual: chirality pdb=" C3' A A1823 " pdb=" C4' A A1823 " pdb=" O3' A A1823 " pdb=" C2' A A1823 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB ILE g 94 " pdb=" CA ILE g 94 " pdb=" CG1 ILE g 94 " pdb=" CG2 ILE g 94 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C3' A A2457 " pdb=" C4' A A2457 " pdb=" O3' A A2457 " pdb=" C2' A A2457 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 18859 not shown) Planarity restraints: 14202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN J 84 " 0.060 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO J 85 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO J 85 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO J 85 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO J 33 " 0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO J 34 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO J 34 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO J 34 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 207 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C ILE D 207 " 0.057 2.00e-02 2.50e+03 pdb=" O ILE D 207 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG D 208 " -0.019 2.00e-02 2.50e+03 ... (remaining 14199 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 2 1.99 - 2.72: 9073 2.72 - 3.45: 133056 3.45 - 4.17: 299754 4.17 - 4.90: 467892 Nonbonded interactions: 909777 Sorted by model distance: nonbonded pdb=" C UNKY2 29 " pdb=" O3' A G 73 " model vdw 1.265 3.270 nonbonded pdb=" CA UNKY2 29 " pdb=" O3' A G 73 " model vdw 1.938 3.470 nonbonded pdb=" OP1 U A2035 " pdb="MG MG A3361 " model vdw 2.007 2.170 nonbonded pdb=" OP1 C A2915 " pdb="MG MG A3361 " model vdw 2.017 2.170 nonbonded pdb=" OP1 C A2100 " pdb="MG MG A3387 " model vdw 2.034 2.170 ... (remaining 909772 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 'G' selection = chain 'x' } ncs_group { reference = (chain 'Y2' and resid 2 through 29) selection = chain 't' selection = (chain 'y' and resid 5 through 32) } 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=0.32 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 28.120 Check model and map are aligned: 1.220 Set scattering table: 0.740 Process input model: 300.640 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 343.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 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 : 0.009 0.097 111955 Z= 0.547 Angle : 0.993 47.991 159485 Z= 0.527 Chirality : 0.052 0.402 18862 Planarity : 0.007 0.091 14202 Dihedral : 20.902 179.956 52806 Min Nonbonded Distance : 1.265 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.19 % Favored : 94.65 % Rotamer: Outliers : 0.84 % Allowed : 9.48 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.01 % Twisted Proline : 0.35 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.07), residues: 8383 helix: -4.57 (0.04), residues: 2662 sheet: -2.07 (0.14), residues: 1091 loop : -2.07 (0.08), residues: 4630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP 6 235 HIS 0.017 0.002 HIS N 237 PHE 0.029 0.003 PHE 6 258 TYR 0.039 0.003 TYR M 222 ARG 0.014 0.001 ARG o 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1777 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1717 time to evaluate : 7.290 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: D 157 MET cc_start: 0.8086 (ttm) cc_final: 0.7782 (ttm) REVERT: D 194 ASN cc_start: 0.8437 (p0) cc_final: 0.8088 (p0) REVERT: D 198 SER cc_start: 0.7018 (t) cc_final: 0.6769 (p) REVERT: E 107 MET cc_start: 0.8051 (ptm) cc_final: 0.7607 (ptp) REVERT: E 180 ASN cc_start: 0.8115 (m-40) cc_final: 0.7787 (m-40) REVERT: E 181 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7627 (tt) REVERT: E 193 LEU cc_start: 0.8292 (mt) cc_final: 0.8008 (mt) REVERT: E 335 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6531 (mm-30) REVERT: I 52 GLU cc_start: 0.7038 (tp30) cc_final: 0.6646 (mm-30) REVERT: I 144 LEU cc_start: 0.5293 (tp) cc_final: 0.4780 (tp) REVERT: J 157 LYS cc_start: 0.4281 (pttp) cc_final: 0.3780 (ttpp) REVERT: K 10 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8328 (tm-30) REVERT: K 25 MET cc_start: 0.7294 (mmm) cc_final: 0.6603 (mmt) REVERT: K 55 ASP cc_start: 0.7012 (m-30) cc_final: 0.6697 (m-30) REVERT: L 81 LYS cc_start: 0.7888 (ptpp) cc_final: 0.7550 (mtmm) REVERT: L 120 LYS cc_start: 0.7187 (tttp) cc_final: 0.6908 (tttt) REVERT: M 35 LYS cc_start: 0.8024 (mtpt) cc_final: 0.7807 (mttm) REVERT: M 54 LYS cc_start: 0.6627 (mttp) cc_final: 0.5485 (pttt) REVERT: M 182 ARG cc_start: 0.7732 (ttt90) cc_final: 0.7512 (ttt-90) REVERT: M 185 ASP cc_start: 0.6843 (t0) cc_final: 0.6508 (t0) REVERT: N 55 ARG cc_start: 0.7179 (mtp180) cc_final: 0.6794 (mtt180) REVERT: N 68 ASN cc_start: 0.8207 (p0) cc_final: 0.7728 (p0) REVERT: N 105 MET cc_start: 0.8222 (mtm) cc_final: 0.7990 (mtm) REVERT: N 233 TYR cc_start: 0.7704 (m-80) cc_final: 0.6887 (m-80) REVERT: O 61 ASP cc_start: 0.8243 (m-30) cc_final: 0.8031 (m-30) REVERT: O 70 GLU cc_start: 0.6233 (tp30) cc_final: 0.5971 (tp30) REVERT: O 71 ARG cc_start: 0.6402 (tmt-80) cc_final: 0.6198 (tpt170) REVERT: O 73 MET cc_start: 0.7944 (tpp) cc_final: 0.7486 (tpt) REVERT: O 124 GLU cc_start: 0.7960 (pt0) cc_final: 0.7757 (pt0) REVERT: P 58 LEU cc_start: 0.8427 (mt) cc_final: 0.8032 (mt) REVERT: P 86 THR cc_start: 0.7809 (p) cc_final: 0.7229 (p) REVERT: Q 120 THR cc_start: 0.7734 (m) cc_final: 0.7441 (m) REVERT: Q 243 ILE cc_start: 0.8271 (mm) cc_final: 0.7962 (mm) REVERT: R 44 ARG cc_start: 0.8324 (mtt90) cc_final: 0.8071 (mtm-85) REVERT: S 81 LYS cc_start: 0.8148 (tttt) cc_final: 0.7622 (tttm) REVERT: S 114 ILE cc_start: 0.8596 (mm) cc_final: 0.8366 (mm) REVERT: S 181 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8387 (ttpt) REVERT: S 195 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8160 (mp) REVERT: T 144 GLU cc_start: 0.7403 (tp30) cc_final: 0.7112 (mm-30) REVERT: T 180 GLU cc_start: 0.7597 (tt0) cc_final: 0.7339 (tt0) REVERT: T 209 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8259 (t) REVERT: U 62 ASN cc_start: 0.7491 (m110) cc_final: 0.7228 (m-40) REVERT: U 129 MET cc_start: 0.6209 (mpp) cc_final: 0.5829 (mtm) REVERT: V 92 ASN cc_start: 0.7939 (t0) cc_final: 0.7718 (t0) REVERT: V 136 ARG cc_start: 0.6299 (mtt180) cc_final: 0.5389 (tpp-160) REVERT: W 102 GLU cc_start: 0.7822 (mp0) cc_final: 0.7445 (mp0) REVERT: X 74 GLU cc_start: 0.6280 (mp0) cc_final: 0.6037 (mp0) REVERT: X 99 LYS cc_start: 0.8166 (ttmm) cc_final: 0.7957 (tttp) REVERT: X 124 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8146 (t) REVERT: X 156 LYS cc_start: 0.7966 (tppt) cc_final: 0.7762 (tptp) REVERT: Y 237 LYS cc_start: 0.6262 (tppt) cc_final: 0.5874 (mmtm) REVERT: Z 68 ILE cc_start: 0.8427 (mt) cc_final: 0.8173 (mt) REVERT: Z 136 ASN cc_start: 0.7453 (m-40) cc_final: 0.7160 (m110) REVERT: 2 60 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8070 (ttt-90) REVERT: 3 146 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7427 (mt-10) REVERT: 4 73 LYS cc_start: 0.7935 (mmtp) cc_final: 0.7610 (tppt) REVERT: 6 206 TYR cc_start: 0.6529 (p90) cc_final: 0.6253 (p90) REVERT: 6 265 ILE cc_start: 0.8283 (mt) cc_final: 0.8040 (mp) REVERT: 6 311 MET cc_start: 0.4280 (ttp) cc_final: 0.4063 (ttp) REVERT: 6 377 TYR cc_start: 0.8424 (m-80) cc_final: 0.8204 (m-80) REVERT: 7 193 MET cc_start: 0.5627 (mmm) cc_final: 0.5353 (mmm) REVERT: 8 160 GLU cc_start: 0.1893 (pt0) cc_final: 0.1167 (pt0) REVERT: 8 172 GLU cc_start: 0.5549 (tt0) cc_final: 0.5178 (tt0) REVERT: 9 20 LYS cc_start: 0.7822 (tttm) cc_final: 0.7449 (tmtt) REVERT: 9 55 GLU cc_start: 0.7094 (mp0) cc_final: 0.6800 (mp0) REVERT: 9 98 PRO cc_start: 0.5792 (Cg_exo) cc_final: 0.5580 (Cg_endo) REVERT: 9 120 GLU cc_start: 0.6194 (mm-30) cc_final: 0.5905 (mm-30) REVERT: d 55 GLU cc_start: 0.5209 (tt0) cc_final: 0.5000 (mt-10) REVERT: d 189 LEU cc_start: 0.7081 (mt) cc_final: 0.6743 (mt) REVERT: d 215 ARG cc_start: 0.6851 (ttt-90) cc_final: 0.6489 (ttt-90) REVERT: d 281 MET cc_start: 0.8176 (tmm) cc_final: 0.7608 (ttp) REVERT: d 287 LEU cc_start: 0.7205 (mt) cc_final: 0.6897 (mt) REVERT: e 53 LEU cc_start: 0.4212 (tp) cc_final: 0.3738 (tp) REVERT: e 249 LYS cc_start: 0.4313 (mttp) cc_final: 0.3239 (mmmt) REVERT: f 58 LYS cc_start: 0.8163 (ptpt) cc_final: 0.7869 (ptmm) REVERT: i 57 TYR cc_start: 0.8444 (m-80) cc_final: 0.8110 (m-10) REVERT: j 26 GLN cc_start: 0.8078 (tp40) cc_final: 0.7766 (mm110) REVERT: k 93 HIS cc_start: 0.6910 (m-70) cc_final: 0.6642 (m170) REVERT: m 77 MET cc_start: 0.0107 (ttt) cc_final: -0.0309 (ppp) REVERT: o 59 GLU cc_start: 0.7624 (pt0) cc_final: 0.7401 (pt0) REVERT: p 100 GLU cc_start: 0.6521 (tt0) cc_final: 0.6218 (tt0) REVERT: p 157 MET cc_start: 0.7100 (mtm) cc_final: 0.6777 (mtp) REVERT: q 56 TYR cc_start: 0.8572 (t80) cc_final: 0.8364 (t80) REVERT: q 85 LEU cc_start: 0.7891 (mt) cc_final: 0.7676 (mt) REVERT: r 48 ILE cc_start: 0.5989 (tp) cc_final: 0.5769 (tt) REVERT: r 52 ARG cc_start: 0.7007 (ptt180) cc_final: 0.6794 (ptt180) REVERT: r 114 LYS cc_start: 0.8147 (mttt) cc_final: 0.7893 (mttp) REVERT: r 164 LYS cc_start: 0.7596 (mttt) cc_final: 0.6878 (mtpt) REVERT: s 91 TYR cc_start: 0.8388 (m-80) cc_final: 0.7755 (m-80) REVERT: s 174 LEU cc_start: 0.7581 (mt) cc_final: 0.7288 (tt) REVERT: s 301 LEU cc_start: 0.8531 (pp) cc_final: 0.8305 (pt) REVERT: s 348 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6744 (mm-30) REVERT: u 96 MET cc_start: 0.2101 (tpp) cc_final: 0.1159 (ptm) REVERT: w 105 MET cc_start: 0.2488 (tpt) cc_final: 0.2174 (ptp) REVERT: w 122 MET cc_start: 0.3175 (ttt) cc_final: 0.1784 (tpp) REVERT: n 120 MET cc_start: 0.2389 (ttt) cc_final: 0.0949 (mtp) outliers start: 60 outliers final: 29 residues processed: 1762 average time/residue: 1.1452 time to fit residues: 3316.3836 Evaluate side-chains 1256 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1223 time to evaluate : 7.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain S residue 159 THR Chi-restraints excluded: chain S residue 195 ILE Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 6 residue 251 THR Chi-restraints excluded: chain 7 residue 73 THR Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain g residue 43 ASP Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain q residue 46 LEU Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain C residue 233 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 848 optimal weight: 5.9990 chunk 761 optimal weight: 0.8980 chunk 422 optimal weight: 0.0770 chunk 260 optimal weight: 0.6980 chunk 513 optimal weight: 0.8980 chunk 406 optimal weight: 0.6980 chunk 787 optimal weight: 8.9990 chunk 304 optimal weight: 2.9990 chunk 478 optimal weight: 1.9990 chunk 586 optimal weight: 3.9990 chunk 912 optimal weight: 5.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN E 57 ASN E 313 ASN F 58 HIS F 184 GLN F 257 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 HIS I 61 HIS ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 GLN I 151 ASN J 54 ASN K 61 ASN K 64 HIS K 94 GLN L 48 ASN L 52 HIS L 113 ASN N 98 HIS N 210 GLN N 222 ASN P 79 HIS P 87 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 142 ASN Q 262 GLN R 12 ASN R 27 HIS R 30 HIS R 79 HIS R 147 GLN S 118 ASN T 109 ASN T 132 HIS T 133 ASN ** T 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 82 HIS V 82 GLN W 76 HIS X 175 GLN Y 179 HIS Y 191 ASN Y 195 ASN Y 225 ASN Z 107 ASN 0 140 GLN 2 54 GLN 4 95 HIS 5 280 GLN ** 5 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 302 HIS 5 353 HIS 5 367 ASN 5 385 HIS ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 295 GLN 6 307 HIS 6 359 HIS 6 361 GLN ** 7 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 127 GLN 8 167 ASN 9 123 GLN b 27 GLN b 129 GLN c 42 GLN c 260 GLN d 207 ASN ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 251 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 251 HIS ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 111 HIS f 112 ASN g 93 ASN g 155 GLN h 87 GLN j 31 GLN j 102 GLN k 15 GLN k 26 ASN k 46 ASN l 135 ASN p 104 HIS p 176 HIS p 184 ASN q 134 ASN r 62 ASN r 112 HIS r 148 ASN ** r 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 239 ASN s 319 GLN v 43 GLN v 63 ASN w 115 GLN ** n 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 111955 Z= 0.189 Angle : 0.650 40.946 159485 Z= 0.328 Chirality : 0.039 0.282 18862 Planarity : 0.005 0.067 14202 Dihedral : 21.548 179.986 34929 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 2.23 % Allowed : 13.71 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.01 % Twisted Proline : 0.35 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.08), residues: 8383 helix: -2.33 (0.08), residues: 2721 sheet: -1.62 (0.14), residues: 1128 loop : -1.47 (0.09), residues: 4534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 2 66 HIS 0.009 0.001 HIS 6 307 PHE 0.021 0.001 PHE 6 298 TYR 0.025 0.001 TYR e 84 ARG 0.010 0.001 ARG 1 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1567 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1403 time to evaluate : 7.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 157 MET cc_start: 0.8096 (ttm) cc_final: 0.7825 (ttm) REVERT: D 198 SER cc_start: 0.7141 (t) cc_final: 0.6941 (p) REVERT: D 232 ARG cc_start: 0.7270 (ttt180) cc_final: 0.7013 (ttt-90) REVERT: E 107 MET cc_start: 0.8088 (ptm) cc_final: 0.7708 (ptp) REVERT: E 193 LEU cc_start: 0.8445 (mt) cc_final: 0.8214 (mt) REVERT: F 189 ILE cc_start: 0.8898 (mt) cc_final: 0.8381 (mm) REVERT: F 223 HIS cc_start: 0.7816 (t70) cc_final: 0.7609 (t70) REVERT: I 37 ARG cc_start: 0.7655 (mtp85) cc_final: 0.7454 (mtt90) REVERT: I 52 GLU cc_start: 0.7062 (tp30) cc_final: 0.6693 (mm-30) REVERT: K 25 MET cc_start: 0.7314 (mmm) cc_final: 0.6643 (mmt) REVERT: K 55 ASP cc_start: 0.7047 (m-30) cc_final: 0.6539 (m-30) REVERT: L 81 LYS cc_start: 0.7660 (ptpp) cc_final: 0.7373 (mtmm) REVERT: M 21 ARG cc_start: 0.7672 (ptp90) cc_final: 0.7364 (ptp90) REVERT: M 54 LYS cc_start: 0.6777 (mttp) cc_final: 0.5413 (pttm) REVERT: M 185 ASP cc_start: 0.6798 (t0) cc_final: 0.6539 (t0) REVERT: N 65 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6824 (mt-10) REVERT: N 68 ASN cc_start: 0.8146 (p0) cc_final: 0.7756 (p0) REVERT: N 105 MET cc_start: 0.8268 (mtm) cc_final: 0.7998 (mtm) REVERT: N 233 TYR cc_start: 0.7666 (m-80) cc_final: 0.6956 (m-80) REVERT: P 58 LEU cc_start: 0.8257 (mt) cc_final: 0.7831 (mt) REVERT: P 173 ARG cc_start: 0.7113 (mtp180) cc_final: 0.6885 (mtp180) REVERT: Q 120 THR cc_start: 0.7904 (m) cc_final: 0.7512 (m) REVERT: Q 158 GLN cc_start: 0.8598 (tp40) cc_final: 0.8350 (tp40) REVERT: Q 243 ILE cc_start: 0.8110 (mm) cc_final: 0.7862 (mt) REVERT: R 44 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7837 (mtm-85) REVERT: S 114 ILE cc_start: 0.8523 (mm) cc_final: 0.8257 (mm) REVERT: S 181 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8403 (tttm) REVERT: T 144 GLU cc_start: 0.7541 (tp30) cc_final: 0.7005 (mm-30) REVERT: T 180 GLU cc_start: 0.7367 (tt0) cc_final: 0.7153 (tt0) REVERT: U 62 ASN cc_start: 0.7493 (m110) cc_final: 0.7279 (m-40) REVERT: V 136 ARG cc_start: 0.6255 (mtt180) cc_final: 0.5339 (tpp-160) REVERT: X 99 LYS cc_start: 0.8317 (ttmm) cc_final: 0.7978 (ttmm) REVERT: X 124 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7823 (t) REVERT: X 196 ILE cc_start: 0.8093 (mt) cc_final: 0.7864 (tp) REVERT: Y 69 ASP cc_start: 0.6523 (OUTLIER) cc_final: 0.5963 (p0) REVERT: Y 237 LYS cc_start: 0.6187 (tppt) cc_final: 0.5628 (mmtm) REVERT: Z 136 ASN cc_start: 0.7514 (m-40) cc_final: 0.7203 (m110) REVERT: 2 72 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7679 (m) REVERT: 3 146 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7104 (mt-10) REVERT: 4 73 LYS cc_start: 0.7854 (mmtp) cc_final: 0.7582 (tppt) REVERT: 6 136 ARG cc_start: 0.6811 (tpt-90) cc_final: 0.6534 (tpt-90) REVERT: 6 185 MET cc_start: 0.6787 (tpp) cc_final: 0.6465 (tpp) REVERT: 7 44 ARG cc_start: 0.6329 (mtt90) cc_final: 0.6103 (mmt90) REVERT: 7 193 MET cc_start: 0.5560 (mmm) cc_final: 0.5329 (mmm) REVERT: 9 20 LYS cc_start: 0.7864 (tttm) cc_final: 0.7562 (tmtt) REVERT: 9 55 GLU cc_start: 0.7029 (mp0) cc_final: 0.6711 (mp0) REVERT: a 111 GLN cc_start: 0.8036 (tt0) cc_final: 0.7558 (tt0) REVERT: d 189 LEU cc_start: 0.6939 (mt) cc_final: 0.6656 (mt) REVERT: d 215 ARG cc_start: 0.6986 (ttt-90) cc_final: 0.6533 (ttt-90) REVERT: d 281 MET cc_start: 0.7963 (tmm) cc_final: 0.7701 (ttp) REVERT: e 249 LYS cc_start: 0.4602 (mttp) cc_final: 0.3476 (mmmt) REVERT: e 275 PHE cc_start: 0.4774 (p90) cc_final: 0.4456 (p90) REVERT: i 57 TYR cc_start: 0.8337 (m-80) cc_final: 0.8133 (m-10) REVERT: j 60 MET cc_start: 0.7411 (mtm) cc_final: 0.7101 (mtm) REVERT: l 123 LYS cc_start: 0.7667 (ttmt) cc_final: 0.7396 (tttt) REVERT: m 77 MET cc_start: 0.0324 (ttt) cc_final: -0.0175 (ppp) REVERT: o 72 GLU cc_start: 0.6156 (mt-10) cc_final: 0.5934 (mt-10) REVERT: p 157 MET cc_start: 0.7323 (mtm) cc_final: 0.6995 (mtp) REVERT: p 176 HIS cc_start: 0.5917 (t-90) cc_final: 0.5617 (t-170) REVERT: p 186 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.6103 (mp0) REVERT: q 125 MET cc_start: 0.7849 (mmm) cc_final: 0.7539 (mmm) REVERT: r 114 LYS cc_start: 0.8172 (mttt) cc_final: 0.7873 (mttp) REVERT: s 91 TYR cc_start: 0.8284 (m-80) cc_final: 0.7821 (m-80) REVERT: s 108 TYR cc_start: 0.7485 (t80) cc_final: 0.7211 (t80) REVERT: s 179 GLN cc_start: 0.7374 (mm-40) cc_final: 0.6873 (mm-40) REVERT: u 96 MET cc_start: 0.2017 (tpp) cc_final: 0.0845 (ptm) REVERT: w 105 MET cc_start: 0.3270 (tpt) cc_final: 0.2595 (ptp) REVERT: n 24 GLU cc_start: 0.1776 (tp30) cc_final: 0.0459 (tm-30) REVERT: n 120 MET cc_start: 0.2391 (ttt) cc_final: 0.0936 (mtp) REVERT: n 189 ILE cc_start: 0.1901 (mt) cc_final: 0.1660 (mm) outliers start: 164 outliers final: 104 residues processed: 1492 average time/residue: 0.9978 time to fit residues: 2488.7065 Evaluate side-chains 1328 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1220 time to evaluate : 7.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain J residue 30 MET Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 121 ASN Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 142 ASN Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 80 ILE Chi-restraints excluded: chain V residue 132 GLU Chi-restraints excluded: chain V residue 204 ILE Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 192 LYS Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 144 LYS Chi-restraints excluded: chain Z residue 142 THR Chi-restraints excluded: chain 0 residue 89 VAL Chi-restraints excluded: chain 0 residue 153 THR Chi-restraints excluded: chain 0 residue 161 THR Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 2 residue 72 THR Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 348 ASP Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 6 residue 295 GLN Chi-restraints excluded: chain 6 residue 321 CYS Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 73 THR Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain d residue 175 ASP Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 43 ASP Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 43 LEU Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 104 ARG Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain s residue 64 GLU Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 307 ARG Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 371 CYS Chi-restraints excluded: chain s residue 411 LYS Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain w residue 139 MET Chi-restraints excluded: chain n residue 222 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 233 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 507 optimal weight: 3.9990 chunk 283 optimal weight: 0.0010 chunk 759 optimal weight: 2.9990 chunk 621 optimal weight: 7.9990 chunk 251 optimal weight: 2.9990 chunk 914 optimal weight: 9.9990 chunk 987 optimal weight: 9.9990 chunk 814 optimal weight: 8.9990 chunk 906 optimal weight: 10.0000 chunk 311 optimal weight: 3.9990 chunk 733 optimal weight: 4.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 280 HIS F 223 HIS F 257 GLN I 61 HIS I 150 HIS K 80 HIS K 94 GLN K 140 ASN L 33 GLN L 52 HIS L 59 HIS ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN M 198 GLN O 39 HIS O 112 ASN O 128 ASN P 121 ASN Q 262 GLN R 89 ASN S 118 ASN T 62 GLN T 75 HIS V 82 GLN X 215 GLN X 237 GLN Y 147 GLN Y 157 GLN ** Y 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 140 GLN 5 195 HIS 5 251 HIS 5 280 GLN 5 289 HIS ** 5 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 384 GLN ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 307 HIS 6 332 HIS 7 207 HIS ** 7 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 103 GLN ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 111 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 92 ASN f 94 HIS ** f 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 155 GLN h 85 ASN i 108 HIS ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 130 GLN q 139 GLN r 184 ASN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 164 HIS ** s 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 239 ASN s 280 ASN ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 156 HIS w 142 GLN ** n 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 111955 Z= 0.531 Angle : 0.855 42.306 159485 Z= 0.424 Chirality : 0.050 0.451 18862 Planarity : 0.007 0.110 14202 Dihedral : 21.666 179.027 34916 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.30 % Favored : 94.64 % Rotamer: Outliers : 4.37 % Allowed : 16.51 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.08), residues: 8383 helix: -1.43 (0.09), residues: 2732 sheet: -1.50 (0.14), residues: 1168 loop : -1.29 (0.09), residues: 4483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP X 9 HIS 0.014 0.003 HIS 1 45 PHE 0.029 0.003 PHE U 24 TYR 0.037 0.003 TYR D 206 ARG 0.012 0.001 ARG 1 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1536 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 1212 time to evaluate : 8.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 198 SER cc_start: 0.6931 (t) cc_final: 0.6708 (p) REVERT: E 282 ILE cc_start: 0.9017 (mm) cc_final: 0.8774 (mm) REVERT: E 284 TYR cc_start: 0.8595 (m-80) cc_final: 0.8290 (m-80) REVERT: E 330 GLU cc_start: 0.6035 (tp30) cc_final: 0.5753 (tp30) REVERT: F 228 GLN cc_start: 0.6970 (tp-100) cc_final: 0.6618 (mm110) REVERT: I 90 PHE cc_start: 0.5108 (OUTLIER) cc_final: 0.3368 (m-10) REVERT: J 51 LYS cc_start: 0.3136 (mttt) cc_final: 0.2516 (tttt) REVERT: J 157 LYS cc_start: 0.4189 (pttp) cc_final: 0.3118 (ttpp) REVERT: K 25 MET cc_start: 0.7648 (mmm) cc_final: 0.7016 (mmt) REVERT: L 128 ARG cc_start: 0.5367 (mpt-90) cc_final: 0.5106 (mtm110) REVERT: L 140 ILE cc_start: 0.8152 (mt) cc_final: 0.7923 (mt) REVERT: M 21 ARG cc_start: 0.7814 (ptp90) cc_final: 0.7600 (ptp90) REVERT: M 54 LYS cc_start: 0.7095 (mttp) cc_final: 0.5833 (pttt) REVERT: M 97 SER cc_start: 0.8778 (p) cc_final: 0.8532 (t) REVERT: M 142 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6171 (pt0) REVERT: M 246 ASP cc_start: 0.6662 (OUTLIER) cc_final: 0.5613 (p0) REVERT: M 249 LYS cc_start: 0.6996 (mmmt) cc_final: 0.6093 (mtpt) REVERT: N 105 MET cc_start: 0.8425 (mtm) cc_final: 0.8222 (mtm) REVERT: O 71 ARG cc_start: 0.6515 (tmt-80) cc_final: 0.6165 (tpt170) REVERT: P 58 LEU cc_start: 0.8396 (mt) cc_final: 0.8015 (mt) REVERT: Q 175 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7382 (pt0) REVERT: T 142 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8541 (mp) REVERT: T 146 THR cc_start: 0.8507 (p) cc_final: 0.8107 (t) REVERT: U 28 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8306 (pt) REVERT: V 136 ARG cc_start: 0.6544 (mtt180) cc_final: 0.5302 (tpp-160) REVERT: V 172 ASP cc_start: 0.6698 (m-30) cc_final: 0.6324 (m-30) REVERT: V 202 MET cc_start: 0.7121 (mtp) cc_final: 0.6709 (mtp) REVERT: W 57 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7175 (tp30) REVERT: X 6 TYR cc_start: 0.8508 (m-80) cc_final: 0.8184 (m-80) REVERT: X 99 LYS cc_start: 0.8343 (ttmm) cc_final: 0.7874 (ttmm) REVERT: X 196 ILE cc_start: 0.8146 (mt) cc_final: 0.7925 (pt) REVERT: X 238 LEU cc_start: 0.5823 (OUTLIER) cc_final: 0.5462 (mt) REVERT: Y 69 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.5976 (p0) REVERT: Y 232 LYS cc_start: 0.7677 (mmtt) cc_final: 0.7136 (mmtm) REVERT: Z 136 ASN cc_start: 0.7487 (m-40) cc_final: 0.7084 (m110) REVERT: 5 355 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8009 (tp) REVERT: 6 150 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7059 (ptp90) REVERT: 6 185 MET cc_start: 0.6750 (tpp) cc_final: 0.6443 (tpp) REVERT: 7 97 GLU cc_start: 0.6970 (tt0) cc_final: 0.6768 (pt0) REVERT: 7 160 ASP cc_start: 0.4676 (t0) cc_final: 0.4418 (t0) REVERT: 7 193 MET cc_start: 0.5409 (mmm) cc_final: 0.5080 (mmm) REVERT: 8 118 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.5994 (mm) REVERT: 8 140 LEU cc_start: 0.5158 (OUTLIER) cc_final: 0.4408 (tp) REVERT: 9 101 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.6047 (mm-30) REVERT: c 62 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: c 227 GLU cc_start: 0.7805 (mp0) cc_final: 0.7353 (mp0) REVERT: c 279 LYS cc_start: 0.6556 (mttt) cc_final: 0.6308 (mtpt) REVERT: d 281 MET cc_start: 0.8000 (tmm) cc_final: 0.7616 (ttp) REVERT: e 53 LEU cc_start: 0.4790 (tp) cc_final: 0.4492 (tt) REVERT: h 58 ARG cc_start: 0.7179 (ttm110) cc_final: 0.6859 (ttm110) REVERT: h 77 VAL cc_start: 0.6557 (OUTLIER) cc_final: 0.6351 (t) REVERT: i 53 MET cc_start: 0.7583 (mmt) cc_final: 0.6709 (mmt) REVERT: j 60 MET cc_start: 0.7984 (mtm) cc_final: 0.7733 (mtm) REVERT: j 84 MET cc_start: 0.8128 (mtp) cc_final: 0.7646 (mtm) REVERT: m 45 ARG cc_start: 0.5016 (mtt180) cc_final: 0.4603 (mmt-90) REVERT: m 77 MET cc_start: 0.0392 (ttt) cc_final: -0.0488 (ppp) REVERT: o 45 ASN cc_start: 0.8413 (m-40) cc_final: 0.8199 (m110) REVERT: o 59 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7351 (pt0) REVERT: p 157 MET cc_start: 0.7277 (mtm) cc_final: 0.6385 (mtp) REVERT: p 186 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5657 (mp0) REVERT: r 89 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7944 (mp) REVERT: r 114 LYS cc_start: 0.8012 (mttt) cc_final: 0.7721 (mttp) REVERT: s 91 TYR cc_start: 0.8486 (m-80) cc_final: 0.7937 (m-80) REVERT: s 411 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6423 (ptpp) REVERT: w 105 MET cc_start: 0.2494 (tpt) cc_final: 0.1816 (ptp) REVERT: w 122 MET cc_start: 0.3366 (ttt) cc_final: 0.2027 (mmm) REVERT: n 24 GLU cc_start: 0.1855 (tp30) cc_final: 0.1322 (pp20) REVERT: n 120 MET cc_start: 0.2108 (ttt) cc_final: 0.0508 (mtp) REVERT: C 204 HIS cc_start: 0.2251 (OUTLIER) cc_final: 0.2010 (m170) outliers start: 324 outliers final: 217 residues processed: 1421 average time/residue: 0.9671 time to fit residues: 2324.9997 Evaluate side-chains 1359 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1121 time to evaluate : 7.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 30 MET Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 142 GLU Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 172 VAL Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 121 ASN Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 175 GLN Chi-restraints excluded: chain Q residue 198 SER Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 111 GLU Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 80 ILE Chi-restraints excluded: chain V residue 92 ASN Chi-restraints excluded: chain V residue 176 ASP Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 141 THR Chi-restraints excluded: chain X residue 12 LYS Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 192 LYS Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 144 LYS Chi-restraints excluded: chain Y residue 158 THR Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 142 THR Chi-restraints excluded: chain 0 residue 89 VAL Chi-restraints excluded: chain 0 residue 108 ASP Chi-restraints excluded: chain 0 residue 131 CYS Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 161 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 1 residue 47 ASP Chi-restraints excluded: chain 3 residue 106 THR Chi-restraints excluded: chain 4 residue 76 CYS Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 153 CYS Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 222 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 348 ASP Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 5 residue 409 GLU Chi-restraints excluded: chain 5 residue 410 THR Chi-restraints excluded: chain 6 residue 63 GLN Chi-restraints excluded: chain 6 residue 150 ARG Chi-restraints excluded: chain 6 residue 151 LEU Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 215 THR Chi-restraints excluded: chain 6 residue 297 THR Chi-restraints excluded: chain 6 residue 300 THR Chi-restraints excluded: chain 6 residue 310 THR Chi-restraints excluded: chain 6 residue 321 CYS Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 7 residue 73 THR Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 120 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 172 VAL Chi-restraints excluded: chain 7 residue 175 ILE Chi-restraints excluded: chain 7 residue 275 CYS Chi-restraints excluded: chain 8 residue 111 THR Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 101 GLU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 66 ASP Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain c residue 62 GLU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain d residue 147 GLU Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 176 ILE Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 187 THR Chi-restraints excluded: chain e residue 237 LEU Chi-restraints excluded: chain f residue 152 THR Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 146 THR Chi-restraints excluded: chain g residue 156 GLU Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 43 LEU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain p residue 121 ILE Chi-restraints excluded: chain p residue 122 THR Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 149 ASP Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain q residue 136 GLN Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain r residue 186 CYS Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 64 GLU Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 263 THR Chi-restraints excluded: chain s residue 301 LEU Chi-restraints excluded: chain s residue 352 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 410 VAL Chi-restraints excluded: chain s residue 411 LYS Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain u residue 101 LEU Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain w residue 100 VAL Chi-restraints excluded: chain w residue 140 CYS Chi-restraints excluded: chain n residue 222 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 233 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 903 optimal weight: 3.9990 chunk 687 optimal weight: 9.9990 chunk 474 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 436 optimal weight: 3.9990 chunk 613 optimal weight: 4.9990 chunk 917 optimal weight: 2.9990 chunk 971 optimal weight: 2.9990 chunk 479 optimal weight: 3.9990 chunk 869 optimal weight: 4.9990 chunk 261 optimal weight: 0.5980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 257 GLN K 94 GLN ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 198 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN Y 147 GLN ** Y 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 140 GLN 5 149 ASN 5 338 GLN ** 5 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 307 HIS ** 7 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 92 ASN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 138 GLN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 239 ASN ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 387 ASN n 44 HIS ** n 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 111955 Z= 0.386 Angle : 0.727 43.113 159485 Z= 0.361 Chirality : 0.045 0.377 18862 Planarity : 0.006 0.076 14202 Dihedral : 21.585 178.822 34912 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.71 % Favored : 95.23 % Rotamer: Outliers : 4.59 % Allowed : 18.13 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.01 % Twisted Proline : 0.18 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.09), residues: 8383 helix: -0.89 (0.09), residues: 2741 sheet: -1.39 (0.14), residues: 1157 loop : -1.13 (0.09), residues: 4485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP d 183 HIS 0.008 0.002 HIS 6 307 PHE 0.038 0.002 PHE 6 270 TYR 0.027 0.002 TYR D 206 ARG 0.012 0.001 ARG s 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1519 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 1179 time to evaluate : 7.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 194 ASN cc_start: 0.8433 (p0) cc_final: 0.8133 (p0) REVERT: F 72 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: F 228 GLN cc_start: 0.6964 (tp-100) cc_final: 0.6671 (mm110) REVERT: H 64 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7679 (pt) REVERT: H 84 GLU cc_start: 0.7298 (tt0) cc_final: 0.7009 (tt0) REVERT: I 144 LEU cc_start: 0.6159 (tp) cc_final: 0.5789 (tp) REVERT: K 25 MET cc_start: 0.7656 (mmm) cc_final: 0.7012 (mmt) REVERT: L 64 ASN cc_start: 0.7294 (OUTLIER) cc_final: 0.7041 (p0) REVERT: L 128 ARG cc_start: 0.5359 (mpt-90) cc_final: 0.5095 (mtt90) REVERT: L 140 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7798 (mt) REVERT: M 54 LYS cc_start: 0.6938 (mttp) cc_final: 0.5480 (pttm) REVERT: M 97 SER cc_start: 0.8719 (p) cc_final: 0.8482 (t) REVERT: M 246 ASP cc_start: 0.6611 (OUTLIER) cc_final: 0.5661 (p0) REVERT: M 249 LYS cc_start: 0.7003 (mmmt) cc_final: 0.6071 (mtpt) REVERT: N 67 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7952 (ptpp) REVERT: N 105 MET cc_start: 0.8314 (mtm) cc_final: 0.8060 (mtm) REVERT: N 173 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7300 (mt0) REVERT: O 123 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8210 (tt) REVERT: P 58 LEU cc_start: 0.8391 (mt) cc_final: 0.8002 (mt) REVERT: P 144 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6685 (ptp) REVERT: S 181 LYS cc_start: 0.8956 (ttpt) cc_final: 0.8391 (tttm) REVERT: T 142 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8469 (mp) REVERT: U 28 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8095 (pt) REVERT: V 21 TYR cc_start: 0.7734 (m-80) cc_final: 0.7302 (m-80) REVERT: V 172 ASP cc_start: 0.6803 (m-30) cc_final: 0.6458 (m-30) REVERT: V 202 MET cc_start: 0.7275 (mtp) cc_final: 0.7024 (mtp) REVERT: W 57 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7033 (tp30) REVERT: X 6 TYR cc_start: 0.8541 (m-80) cc_final: 0.8308 (m-80) REVERT: X 44 ARG cc_start: 0.7950 (ptp-170) cc_final: 0.7489 (mtm110) REVERT: X 99 LYS cc_start: 0.8339 (ttmm) cc_final: 0.7873 (ttmm) REVERT: X 198 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6582 (tt0) REVERT: X 238 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5677 (mt) REVERT: Y 69 ASP cc_start: 0.6418 (OUTLIER) cc_final: 0.5840 (p0) REVERT: Y 232 LYS cc_start: 0.7643 (mmtt) cc_final: 0.7099 (mmtm) REVERT: Z 136 ASN cc_start: 0.7441 (m-40) cc_final: 0.7196 (m110) REVERT: 4 97 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.6299 (mtp85) REVERT: 5 355 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8017 (tp) REVERT: 7 81 MET cc_start: 0.7521 (mmm) cc_final: 0.7127 (mmt) REVERT: 7 160 ASP cc_start: 0.4749 (t0) cc_final: 0.4519 (t0) REVERT: 7 193 MET cc_start: 0.5257 (mmm) cc_final: 0.5033 (mmm) REVERT: 8 140 LEU cc_start: 0.5028 (OUTLIER) cc_final: 0.4516 (tp) REVERT: 9 54 LYS cc_start: 0.7540 (tptp) cc_final: 0.7320 (tppt) REVERT: 9 101 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6361 (mm-30) REVERT: a 111 GLN cc_start: 0.8143 (tt0) cc_final: 0.7770 (tt0) REVERT: b 24 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: c 62 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: c 227 GLU cc_start: 0.7744 (mp0) cc_final: 0.7275 (mp0) REVERT: d 261 MET cc_start: 0.8637 (ttm) cc_final: 0.8276 (ttp) REVERT: d 281 MET cc_start: 0.8036 (tmm) cc_final: 0.7771 (ttp) REVERT: h 58 ARG cc_start: 0.7095 (ttm110) cc_final: 0.6857 (ttm110) REVERT: h 77 VAL cc_start: 0.6839 (OUTLIER) cc_final: 0.6449 (t) REVERT: i 68 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8261 (mtpt) REVERT: j 60 MET cc_start: 0.7974 (mtm) cc_final: 0.7761 (mtm) REVERT: m 45 ARG cc_start: 0.5093 (mtt180) cc_final: 0.4657 (mmt-90) REVERT: m 77 MET cc_start: 0.0337 (ttt) cc_final: -0.0486 (ppp) REVERT: o 45 ASN cc_start: 0.8322 (m-40) cc_final: 0.8097 (m110) REVERT: p 157 MET cc_start: 0.7104 (mtm) cc_final: 0.6828 (mtp) REVERT: p 186 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5686 (mp0) REVERT: r 89 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7757 (mt) REVERT: r 114 LYS cc_start: 0.7949 (mttt) cc_final: 0.7678 (mttp) REVERT: s 91 TYR cc_start: 0.8434 (m-80) cc_final: 0.7893 (m-80) REVERT: s 108 TYR cc_start: 0.7913 (t80) cc_final: 0.7682 (t80) REVERT: u 96 MET cc_start: 0.2393 (tpp) cc_final: 0.1436 (ptm) REVERT: w 122 MET cc_start: 0.3321 (ttt) cc_final: 0.1954 (mmm) REVERT: n 108 MET cc_start: 0.3086 (tmm) cc_final: 0.1174 (mtt) REVERT: n 120 MET cc_start: 0.2120 (ttt) cc_final: 0.0598 (mtp) outliers start: 340 outliers final: 231 residues processed: 1405 average time/residue: 1.0081 time to fit residues: 2407.1428 Evaluate side-chains 1376 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1121 time to evaluate : 7.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 64 ASN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain N residue 61 LYS Chi-restraints excluded: chain N residue 67 LYS Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 121 ASN Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 198 SER Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 111 GLU Chi-restraints excluded: chain S residue 112 ASP Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 167 MET Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 111 PHE Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 80 ILE Chi-restraints excluded: chain V residue 102 MET Chi-restraints excluded: chain V residue 115 LEU Chi-restraints excluded: chain V residue 132 GLU Chi-restraints excluded: chain V residue 176 ASP Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 12 LYS Chi-restraints excluded: chain X residue 60 GLU Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 192 LYS Chi-restraints excluded: chain X residue 198 GLU Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 142 THR Chi-restraints excluded: chain 0 residue 89 VAL Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 131 CYS Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 161 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 1 residue 47 ASP Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 106 THR Chi-restraints excluded: chain 4 residue 76 CYS Chi-restraints excluded: chain 4 residue 97 ARG Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 222 VAL Chi-restraints excluded: chain 5 residue 232 THR Chi-restraints excluded: chain 5 residue 262 ILE Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 348 ASP Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 5 residue 409 GLU Chi-restraints excluded: chain 5 residue 410 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 215 THR Chi-restraints excluded: chain 6 residue 300 THR Chi-restraints excluded: chain 6 residue 307 HIS Chi-restraints excluded: chain 6 residue 310 THR Chi-restraints excluded: chain 6 residue 321 CYS Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 40 LEU Chi-restraints excluded: chain 7 residue 73 THR Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 7 residue 105 LEU Chi-restraints excluded: chain 7 residue 120 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 175 ILE Chi-restraints excluded: chain 7 residue 183 VAL Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 8 residue 111 THR Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 53 ILE Chi-restraints excluded: chain 9 residue 101 GLU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 24 GLN Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain c residue 62 GLU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 142 LYS Chi-restraints excluded: chain d residue 147 GLU Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 264 LEU Chi-restraints excluded: chain f residue 110 VAL Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 146 THR Chi-restraints excluded: chain g residue 156 GLU Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 43 LEU Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain o residue 82 PHE Chi-restraints excluded: chain p residue 52 SER Chi-restraints excluded: chain p residue 122 THR Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 186 CYS Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 64 GLU Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 263 THR Chi-restraints excluded: chain s residue 301 LEU Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 371 CYS Chi-restraints excluded: chain s residue 410 VAL Chi-restraints excluded: chain s residue 411 LYS Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain s residue 425 LEU Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 193 LEU Chi-restraints excluded: chain w residue 100 VAL Chi-restraints excluded: chain w residue 140 CYS Chi-restraints excluded: chain n residue 43 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 233 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 809 optimal weight: 0.1980 chunk 551 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 723 optimal weight: 2.9990 chunk 400 optimal weight: 1.9990 chunk 828 optimal weight: 2.9990 chunk 671 optimal weight: 1.9990 chunk 1 optimal weight: 0.0170 chunk 496 optimal weight: 0.5980 chunk 871 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 257 GLN K 94 GLN ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 ASN L 142 GLN M 198 GLN O 112 ASN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 ASN Q 158 GLN S 118 ASN V 82 GLN ** X 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 147 GLN Y 183 GLN 0 140 GLN 1 35 ASN ** 5 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 338 GLN 5 343 GLN ** 5 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN 7 139 ASN ** 7 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 65 HIS s 239 ASN ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 111955 Z= 0.222 Angle : 0.618 39.179 159485 Z= 0.308 Chirality : 0.040 0.587 18862 Planarity : 0.005 0.055 14202 Dihedral : 21.409 177.969 34911 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 4.05 % Allowed : 19.28 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.01 % 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: -1.24 (0.09), residues: 8383 helix: -0.37 (0.10), residues: 2740 sheet: -1.20 (0.14), residues: 1137 loop : -0.93 (0.09), residues: 4506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP S 106 HIS 0.035 0.001 HIS 6 307 PHE 0.017 0.001 PHE 5 411 TYR 0.023 0.001 TYR e 84 ARG 0.016 0.000 ARG s 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1508 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 1208 time to evaluate : 7.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 194 ASN cc_start: 0.8445 (p0) cc_final: 0.8166 (p0) REVERT: E 67 ASP cc_start: 0.6082 (OUTLIER) cc_final: 0.5752 (t70) REVERT: F 228 GLN cc_start: 0.6895 (tp-100) cc_final: 0.6611 (mm110) REVERT: H 64 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7367 (pt) REVERT: I 90 PHE cc_start: 0.5075 (OUTLIER) cc_final: 0.3404 (m-10) REVERT: K 25 MET cc_start: 0.7635 (mmm) cc_final: 0.6976 (mmt) REVERT: L 81 LYS cc_start: 0.7727 (ptpp) cc_final: 0.7384 (mtmm) REVERT: L 128 ARG cc_start: 0.5253 (mpt-90) cc_final: 0.5014 (mtt90) REVERT: L 140 ILE cc_start: 0.8057 (mt) cc_final: 0.7809 (mt) REVERT: M 54 LYS cc_start: 0.6728 (mttp) cc_final: 0.5365 (pttm) REVERT: M 62 ARG cc_start: 0.7826 (mtm180) cc_final: 0.7609 (mtt180) REVERT: M 249 LYS cc_start: 0.6935 (mmmt) cc_final: 0.6543 (mmtm) REVERT: N 68 ASN cc_start: 0.8200 (p0) cc_final: 0.7954 (p0) REVERT: N 105 MET cc_start: 0.8338 (mtm) cc_final: 0.8096 (mtm) REVERT: N 233 TYR cc_start: 0.7824 (m-80) cc_final: 0.7165 (m-80) REVERT: O 123 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8193 (tt) REVERT: P 58 LEU cc_start: 0.8217 (mt) cc_final: 0.7812 (mt) REVERT: P 165 MET cc_start: 0.7114 (ttm) cc_final: 0.6912 (mmm) REVERT: Q 152 ARG cc_start: 0.8101 (ttt-90) cc_final: 0.7836 (ttt-90) REVERT: Q 204 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6742 (ptm) REVERT: R 44 ARG cc_start: 0.8205 (mtt90) cc_final: 0.7629 (mtt90) REVERT: S 181 LYS cc_start: 0.8755 (ttpt) cc_final: 0.8329 (tttm) REVERT: S 195 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8285 (mp) REVERT: T 87 MET cc_start: 0.8037 (tpt) cc_final: 0.7728 (tpt) REVERT: V 172 ASP cc_start: 0.6634 (m-30) cc_final: 0.6376 (m-30) REVERT: X 33 GLU cc_start: 0.6433 (pp20) cc_final: 0.6202 (tp30) REVERT: X 99 LYS cc_start: 0.8443 (ttmm) cc_final: 0.8164 (tttp) REVERT: X 198 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6562 (tt0) REVERT: X 238 LEU cc_start: 0.5823 (OUTLIER) cc_final: 0.5580 (mt) REVERT: Y 69 ASP cc_start: 0.6250 (OUTLIER) cc_final: 0.5713 (p0) REVERT: Y 137 ASP cc_start: 0.6770 (t0) cc_final: 0.6410 (t0) REVERT: Y 232 LYS cc_start: 0.7627 (mmtt) cc_final: 0.7065 (mmtm) REVERT: Z 136 ASN cc_start: 0.7445 (m-40) cc_final: 0.7182 (m110) REVERT: 1 20 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7576 (mtm) REVERT: 2 68 ARG cc_start: 0.8284 (ttt180) cc_final: 0.8077 (ttt180) REVERT: 5 95 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6877 (mp0) REVERT: 5 246 GLU cc_start: 0.5407 (mm-30) cc_final: 0.4961 (mm-30) REVERT: 6 150 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6854 (ptp90) REVERT: 6 155 TYR cc_start: 0.8435 (m-80) cc_final: 0.7894 (m-80) REVERT: 7 81 MET cc_start: 0.7337 (mmm) cc_final: 0.6965 (mmt) REVERT: 7 143 TRP cc_start: 0.8537 (OUTLIER) cc_final: 0.6620 (m-90) REVERT: 7 193 MET cc_start: 0.5117 (mmm) cc_final: 0.4901 (mmm) REVERT: 7 253 LYS cc_start: 0.6508 (OUTLIER) cc_final: 0.6155 (mttm) REVERT: 8 140 LEU cc_start: 0.5091 (OUTLIER) cc_final: 0.4566 (tp) REVERT: a 111 GLN cc_start: 0.8173 (tt0) cc_final: 0.7789 (tt0) REVERT: c 62 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: c 227 GLU cc_start: 0.7404 (mp0) cc_final: 0.6928 (mp0) REVERT: c 240 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7572 (mp) REVERT: d 189 LEU cc_start: 0.6411 (mt) cc_final: 0.6177 (mt) REVERT: d 261 MET cc_start: 0.8560 (ttm) cc_final: 0.8252 (ttp) REVERT: d 281 MET cc_start: 0.8106 (tmm) cc_final: 0.7824 (ttp) REVERT: h 58 ARG cc_start: 0.6986 (ttm110) cc_final: 0.6684 (ttm110) REVERT: h 122 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.5764 (mmt180) REVERT: i 68 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8179 (mtpt) REVERT: j 60 MET cc_start: 0.7914 (mtm) cc_final: 0.7702 (mtm) REVERT: m 45 ARG cc_start: 0.5087 (mtt180) cc_final: 0.4636 (mmt-90) REVERT: p 186 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5780 (mp0) REVERT: r 114 LYS cc_start: 0.8135 (mttt) cc_final: 0.7843 (mttp) REVERT: s 91 TYR cc_start: 0.8407 (m-80) cc_final: 0.7901 (m-80) REVERT: s 108 TYR cc_start: 0.7767 (t80) cc_final: 0.7549 (t80) REVERT: s 232 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: u 96 MET cc_start: 0.2368 (tpp) cc_final: 0.1457 (ptm) REVERT: w 122 MET cc_start: 0.2670 (ttt) cc_final: 0.2134 (mmm) REVERT: w 123 GLU cc_start: 0.4440 (OUTLIER) cc_final: 0.4180 (mp0) REVERT: w 142 GLN cc_start: 0.2676 (OUTLIER) cc_final: 0.0840 (pt0) REVERT: n 108 MET cc_start: 0.2747 (tmm) cc_final: 0.0856 (mtt) REVERT: n 120 MET cc_start: 0.2102 (ttt) cc_final: 0.1744 (ptm) outliers start: 300 outliers final: 200 residues processed: 1406 average time/residue: 0.9877 time to fit residues: 2347.4990 Evaluate side-chains 1357 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1136 time to evaluate : 7.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain O residue 17 ARG Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain S residue 195 ILE Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 167 MET Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 80 ILE Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 115 LEU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 132 GLU Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 192 LYS Chi-restraints excluded: chain X residue 198 GLU Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Z residue 44 LYS Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain Z residue 142 THR Chi-restraints excluded: chain 0 residue 89 VAL Chi-restraints excluded: chain 0 residue 108 ASP Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 131 CYS Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 161 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 20 MET Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 106 THR Chi-restraints excluded: chain 4 residue 76 CYS Chi-restraints excluded: chain 4 residue 81 LEU Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 153 CYS Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 222 VAL Chi-restraints excluded: chain 5 residue 232 THR Chi-restraints excluded: chain 5 residue 348 ASP Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 5 residue 409 GLU Chi-restraints excluded: chain 6 residue 150 ARG Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 215 THR Chi-restraints excluded: chain 6 residue 251 THR Chi-restraints excluded: chain 6 residue 291 TYR Chi-restraints excluded: chain 6 residue 321 CYS Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 73 THR Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 7 residue 105 LEU Chi-restraints excluded: chain 7 residue 120 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 175 ILE Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 253 LYS Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 8 residue 111 THR Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 133 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain c residue 62 GLU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 283 GLU Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain d residue 147 GLU Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain f residue 110 VAL Chi-restraints excluded: chain f residue 152 THR Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 122 ARG Chi-restraints excluded: chain h residue 156 TRP Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 43 LEU Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain o residue 16 GLN Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain o residue 82 PHE Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 149 ASP Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain r residue 147 LEU Chi-restraints excluded: chain r residue 186 CYS Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 232 GLN Chi-restraints excluded: chain s residue 352 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 410 VAL Chi-restraints excluded: chain s residue 411 LYS Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 193 LEU Chi-restraints excluded: chain w residue 100 VAL Chi-restraints excluded: chain w residue 123 GLU Chi-restraints excluded: chain w residue 140 CYS Chi-restraints excluded: chain w residue 142 GLN Chi-restraints excluded: chain n residue 43 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 233 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 326 optimal weight: 2.9990 chunk 874 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 570 optimal weight: 0.8980 chunk 239 optimal weight: 3.9990 chunk 972 optimal weight: 9.9990 chunk 807 optimal weight: 5.9990 chunk 450 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 321 optimal weight: 0.0980 chunk 510 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 63 GLN F 74 GLN F 257 GLN I 61 HIS K 56 HIS K 94 GLN ** L 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 198 GLN O 100 GLN O 112 ASN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 158 GLN S 118 ASN ** X 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 147 GLN 0 140 GLN 1 35 ASN ** 5 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 165 GLN ** 5 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 338 GLN ** 5 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 266 HIS ** 7 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 42 GLN ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 ASN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 239 ASN ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 358 GLN ** n 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 111955 Z= 0.353 Angle : 0.676 15.304 159485 Z= 0.341 Chirality : 0.044 0.390 18862 Planarity : 0.006 0.082 14202 Dihedral : 21.416 178.380 34910 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.23 % Favored : 94.71 % Rotamer: Outliers : 4.89 % Allowed : 19.53 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.01 % 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: -1.25 (0.09), residues: 8383 helix: -0.33 (0.10), residues: 2759 sheet: -1.23 (0.14), residues: 1182 loop : -0.96 (0.09), residues: 4442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP X 9 HIS 0.007 0.001 HIS E 197 PHE 0.020 0.002 PHE E 316 TYR 0.025 0.002 TYR D 206 ARG 0.014 0.001 ARG s 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1521 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 363 poor density : 1158 time to evaluate : 7.096 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: D 194 ASN cc_start: 0.8455 (p0) cc_final: 0.8189 (p0) REVERT: H 64 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7471 (pt) REVERT: I 90 PHE cc_start: 0.5045 (OUTLIER) cc_final: 0.3296 (m-10) REVERT: K 25 MET cc_start: 0.7688 (mmm) cc_final: 0.7019 (mmt) REVERT: L 64 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.6775 (p0) REVERT: L 128 ARG cc_start: 0.5411 (mpt-90) cc_final: 0.5148 (mtt90) REVERT: M 54 LYS cc_start: 0.6865 (mttp) cc_final: 0.5416 (pttm) REVERT: M 62 ARG cc_start: 0.7921 (mtm180) cc_final: 0.7641 (mtt180) REVERT: M 118 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8109 (mp) REVERT: N 68 ASN cc_start: 0.8189 (p0) cc_final: 0.7960 (p0) REVERT: N 105 MET cc_start: 0.8399 (mtm) cc_final: 0.8168 (mtm) REVERT: N 173 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: N 182 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8450 (mttt) REVERT: O 123 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8146 (tt) REVERT: P 58 LEU cc_start: 0.8281 (mt) cc_final: 0.7923 (mt) REVERT: P 158 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6852 (mmm) REVERT: P 165 MET cc_start: 0.7207 (ttm) cc_final: 0.6988 (mmm) REVERT: Q 175 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7382 (pt0) REVERT: Q 204 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6941 (ptp) REVERT: R 147 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7260 (mm-40) REVERT: S 119 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6356 (tt0) REVERT: S 181 LYS cc_start: 0.8933 (ttpt) cc_final: 0.8375 (tttm) REVERT: T 110 ASP cc_start: 0.6775 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: T 142 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8361 (mt) REVERT: U 28 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8111 (pt) REVERT: V 172 ASP cc_start: 0.6794 (m-30) cc_final: 0.6480 (m-30) REVERT: X 99 LYS cc_start: 0.8372 (ttmm) cc_final: 0.7906 (ttmm) REVERT: X 198 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6580 (tt0) REVERT: Y 69 ASP cc_start: 0.6464 (OUTLIER) cc_final: 0.5855 (p0) REVERT: Y 232 LYS cc_start: 0.7666 (mmtt) cc_final: 0.7064 (mmtm) REVERT: Z 136 ASN cc_start: 0.7443 (m-40) cc_final: 0.7172 (m110) REVERT: 1 20 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7678 (mtm) REVERT: 5 94 HIS cc_start: 0.6346 (OUTLIER) cc_final: 0.5990 (t-90) REVERT: 5 355 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8014 (tp) REVERT: 6 150 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6878 (ptp90) REVERT: 6 155 TYR cc_start: 0.8443 (m-80) cc_final: 0.7944 (m-80) REVERT: 6 323 TRP cc_start: 0.7979 (OUTLIER) cc_final: 0.6764 (t-100) REVERT: 7 81 MET cc_start: 0.7529 (mmm) cc_final: 0.7190 (mmt) REVERT: 7 143 TRP cc_start: 0.8610 (OUTLIER) cc_final: 0.6601 (m-90) REVERT: 7 193 MET cc_start: 0.5197 (mmm) cc_final: 0.4981 (mmm) REVERT: 8 140 LEU cc_start: 0.5087 (OUTLIER) cc_final: 0.4546 (tp) REVERT: 9 102 LYS cc_start: 0.6012 (mmmm) cc_final: 0.5672 (mmtm) REVERT: a 111 GLN cc_start: 0.8195 (tt0) cc_final: 0.7879 (tt0) REVERT: b 24 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: c 62 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: c 227 GLU cc_start: 0.7491 (mp0) cc_final: 0.6998 (mp0) REVERT: c 240 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7668 (mp) REVERT: d 226 ASP cc_start: 0.6629 (OUTLIER) cc_final: 0.6391 (t0) REVERT: d 261 MET cc_start: 0.8677 (ttm) cc_final: 0.8386 (ttp) REVERT: d 281 MET cc_start: 0.8080 (tmm) cc_final: 0.7822 (ttp) REVERT: h 122 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.5839 (mmt180) REVERT: i 68 LYS cc_start: 0.8486 (mtpp) cc_final: 0.8240 (mtpt) REVERT: m 45 ARG cc_start: 0.5031 (mtt180) cc_final: 0.4615 (mmt-90) REVERT: o 45 ASN cc_start: 0.8311 (m-40) cc_final: 0.8083 (m110) REVERT: p 186 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5876 (mp0) REVERT: r 89 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7755 (mt) REVERT: r 114 LYS cc_start: 0.8163 (mttt) cc_final: 0.7888 (mttp) REVERT: s 91 TYR cc_start: 0.8517 (m-80) cc_final: 0.7968 (m-80) REVERT: s 108 TYR cc_start: 0.7919 (t80) cc_final: 0.7585 (t80) REVERT: s 232 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: s 411 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6159 (ptpp) REVERT: w 142 GLN cc_start: 0.2725 (OUTLIER) cc_final: 0.0889 (pt0) REVERT: n 108 MET cc_start: 0.2962 (tmm) cc_final: 0.1180 (mtt) REVERT: n 183 GLU cc_start: 0.3475 (pm20) cc_final: 0.3065 (tt0) REVERT: n 224 ILE cc_start: 0.3678 (mm) cc_final: 0.3357 (pt) REVERT: C 187 GLU cc_start: 0.5009 (OUTLIER) cc_final: 0.3903 (mm-30) REVERT: C 225 VAL cc_start: 0.2315 (OUTLIER) cc_final: 0.1990 (p) outliers start: 363 outliers final: 268 residues processed: 1407 average time/residue: 0.9468 time to fit residues: 2269.7718 Evaluate side-chains 1436 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1132 time to evaluate : 7.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 90 PHE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 64 ASN Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain N residue 61 LYS Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain N residue 182 LYS Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain P residue 158 MET Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 175 GLN Chi-restraints excluded: chain Q residue 198 SER Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 147 GLN Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 110 ASP Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 80 ILE Chi-restraints excluded: chain V residue 86 VAL Chi-restraints excluded: chain V residue 92 ASN Chi-restraints excluded: chain V residue 102 MET Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 115 LEU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 176 ASP Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain X residue 12 LYS Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 192 LYS Chi-restraints excluded: chain X residue 198 GLU Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Z residue 44 LYS Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain Z residue 142 THR Chi-restraints excluded: chain 0 residue 89 VAL Chi-restraints excluded: chain 0 residue 108 ASP Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 131 CYS Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 161 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 20 MET Chi-restraints excluded: chain 1 residue 47 ASP Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 106 THR Chi-restraints excluded: chain 4 residue 76 CYS Chi-restraints excluded: chain 4 residue 81 LEU Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 94 HIS Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 222 VAL Chi-restraints excluded: chain 5 residue 232 THR Chi-restraints excluded: chain 5 residue 262 ILE Chi-restraints excluded: chain 5 residue 320 SER Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 5 residue 409 GLU Chi-restraints excluded: chain 6 residue 143 CYS Chi-restraints excluded: chain 6 residue 150 ARG Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 215 THR Chi-restraints excluded: chain 6 residue 233 LEU Chi-restraints excluded: chain 6 residue 297 THR Chi-restraints excluded: chain 6 residue 302 ASP Chi-restraints excluded: chain 6 residue 310 THR Chi-restraints excluded: chain 6 residue 321 CYS Chi-restraints excluded: chain 6 residue 323 TRP Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 40 LEU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 7 residue 73 THR Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 7 residue 105 LEU Chi-restraints excluded: chain 7 residue 120 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 175 ILE Chi-restraints excluded: chain 7 residue 183 VAL Chi-restraints excluded: chain 7 residue 219 LEU Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 243 LYS Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 8 residue 107 THR Chi-restraints excluded: chain 8 residue 111 THR Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 133 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 24 GLN Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain c residue 62 GLU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 283 GLU Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain d residue 147 GLU Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 172 MET Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 214 VAL Chi-restraints excluded: chain d residue 226 ASP Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 288 LYS Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 237 LEU Chi-restraints excluded: chain f residue 110 VAL Chi-restraints excluded: chain f residue 152 THR Chi-restraints excluded: chain f residue 190 THR Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 122 ARG Chi-restraints excluded: chain h residue 156 TRP Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 43 LEU Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 67 LEU Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain o residue 16 GLN Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain o residue 82 PHE Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 52 SER Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain p residue 122 THR Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 149 ASP Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain q residue 136 GLN Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain r residue 147 LEU Chi-restraints excluded: chain r residue 186 CYS Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 232 GLN Chi-restraints excluded: chain s residue 352 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 410 VAL Chi-restraints excluded: chain s residue 411 LYS Chi-restraints excluded: chain s residue 425 LEU Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 193 LEU Chi-restraints excluded: chain v residue 9 VAL Chi-restraints excluded: chain w residue 100 VAL Chi-restraints excluded: chain w residue 123 GLU Chi-restraints excluded: chain w residue 140 CYS Chi-restraints excluded: chain w residue 142 GLN Chi-restraints excluded: chain n residue 43 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 233 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 937 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 554 optimal weight: 1.9990 chunk 710 optimal weight: 6.9990 chunk 550 optimal weight: 0.7980 chunk 818 optimal weight: 2.9990 chunk 542 optimal weight: 0.5980 chunk 968 optimal weight: 3.9990 chunk 606 optimal weight: 8.9990 chunk 590 optimal weight: 0.0060 chunk 447 optimal weight: 2.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 74 GLN F 257 GLN I 61 HIS K 94 GLN ** L 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 ASN L 142 GLN M 198 GLN O 100 GLN O 112 ASN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 158 GLN R 125 HIS S 118 ASN ** X 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 147 GLN 0 140 GLN 1 35 ASN ** 5 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 338 GLN 5 343 GLN ** 5 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 134 ASN ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 156 ASN ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 239 ASN ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 111955 Z= 0.265 Angle : 0.616 14.948 159485 Z= 0.312 Chirality : 0.041 0.339 18862 Planarity : 0.005 0.059 14202 Dihedral : 21.368 178.965 34908 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.80 % Favored : 95.14 % Rotamer: Outliers : 4.69 % Allowed : 20.03 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.01 % 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: -1.06 (0.09), residues: 8383 helix: -0.16 (0.10), residues: 2760 sheet: -1.12 (0.14), residues: 1166 loop : -0.86 (0.09), residues: 4457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP X 9 HIS 0.015 0.001 HIS 6 307 PHE 0.017 0.002 PHE 5 411 TYR 0.022 0.002 TYR e 84 ARG 0.016 0.001 ARG s 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 1167 time to evaluate : 7.197 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: D 194 ASN cc_start: 0.8436 (p0) cc_final: 0.8172 (p0) REVERT: H 64 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7472 (pt) REVERT: I 90 PHE cc_start: 0.5036 (OUTLIER) cc_final: 0.3322 (m-10) REVERT: I 144 LEU cc_start: 0.6274 (tp) cc_final: 0.5898 (tp) REVERT: J 30 MET cc_start: 0.3806 (tpp) cc_final: 0.3377 (tpp) REVERT: K 25 MET cc_start: 0.7649 (mmm) cc_final: 0.7010 (mmt) REVERT: L 128 ARG cc_start: 0.5356 (mpt-90) cc_final: 0.5124 (mtt90) REVERT: M 54 LYS cc_start: 0.6784 (mttp) cc_final: 0.5336 (pttm) REVERT: M 62 ARG cc_start: 0.7867 (mtm180) cc_final: 0.7656 (mtt180) REVERT: M 118 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8086 (mp) REVERT: N 105 MET cc_start: 0.8400 (mtm) cc_final: 0.8150 (mtm) REVERT: N 173 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7342 (tt0) REVERT: N 233 TYR cc_start: 0.7794 (m-80) cc_final: 0.7099 (m-80) REVERT: P 58 LEU cc_start: 0.8233 (mt) cc_final: 0.7897 (mt) REVERT: R 44 ARG cc_start: 0.8204 (mtt90) cc_final: 0.7725 (mtt90) REVERT: R 147 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7268 (mm-40) REVERT: S 119 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6400 (tt0) REVERT: S 181 LYS cc_start: 0.8899 (ttpt) cc_final: 0.8383 (tttm) REVERT: S 195 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8304 (mp) REVERT: T 110 ASP cc_start: 0.6670 (OUTLIER) cc_final: 0.6459 (m-30) REVERT: T 180 GLU cc_start: 0.7167 (tt0) cc_final: 0.6950 (tt0) REVERT: T 197 LYS cc_start: 0.7951 (mptt) cc_final: 0.7652 (mptt) REVERT: U 28 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8029 (pt) REVERT: V 172 ASP cc_start: 0.6785 (m-30) cc_final: 0.6473 (m-30) REVERT: X 99 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8163 (tttp) REVERT: X 198 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6560 (tt0) REVERT: Y 69 ASP cc_start: 0.6380 (OUTLIER) cc_final: 0.5813 (p0) REVERT: Y 137 ASP cc_start: 0.6739 (t0) cc_final: 0.6397 (t0) REVERT: Y 232 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7058 (mmtm) REVERT: Z 76 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8247 (mtp85) REVERT: Z 98 GLN cc_start: 0.7663 (tp-100) cc_final: 0.7349 (tp-100) REVERT: Z 136 ASN cc_start: 0.7438 (m-40) cc_final: 0.7160 (m110) REVERT: 1 20 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7651 (mtm) REVERT: 5 95 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6869 (mp0) REVERT: 5 246 GLU cc_start: 0.5514 (mm-30) cc_final: 0.5035 (tp30) REVERT: 5 355 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7980 (tp) REVERT: 6 150 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.6930 (ptp90) REVERT: 6 155 TYR cc_start: 0.8452 (m-80) cc_final: 0.7971 (m-80) REVERT: 6 298 PHE cc_start: 0.6075 (OUTLIER) cc_final: 0.5658 (p90) REVERT: 7 81 MET cc_start: 0.7469 (mmm) cc_final: 0.7156 (mmt) REVERT: 7 143 TRP cc_start: 0.8590 (OUTLIER) cc_final: 0.6653 (m-90) REVERT: 7 253 LYS cc_start: 0.6614 (OUTLIER) cc_final: 0.6354 (mttm) REVERT: 8 140 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.4551 (tp) REVERT: a 111 GLN cc_start: 0.8180 (tt0) cc_final: 0.7788 (tt0) REVERT: b 24 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: c 62 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: c 227 GLU cc_start: 0.7408 (mp0) cc_final: 0.6915 (mp0) REVERT: c 240 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7602 (mp) REVERT: d 226 ASP cc_start: 0.6623 (OUTLIER) cc_final: 0.6349 (t0) REVERT: d 261 MET cc_start: 0.8568 (ttm) cc_final: 0.8274 (ttp) REVERT: d 281 MET cc_start: 0.8154 (tmm) cc_final: 0.7874 (ttp) REVERT: h 122 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.5684 (mmt180) REVERT: i 49 GLU cc_start: 0.6798 (tp30) cc_final: 0.6464 (tt0) REVERT: i 68 LYS cc_start: 0.8458 (mtpp) cc_final: 0.8190 (mtpt) REVERT: m 45 ARG cc_start: 0.5053 (mtt180) cc_final: 0.4610 (mmt-90) REVERT: p 186 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.5879 (mp0) REVERT: r 89 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7761 (mt) REVERT: r 114 LYS cc_start: 0.8136 (mttt) cc_final: 0.7848 (mttp) REVERT: s 91 TYR cc_start: 0.8470 (m-80) cc_final: 0.7914 (m-80) REVERT: s 108 TYR cc_start: 0.7829 (t80) cc_final: 0.7610 (t80) REVERT: s 232 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: s 411 LYS cc_start: 0.6827 (OUTLIER) cc_final: 0.6089 (ptpp) REVERT: w 142 GLN cc_start: 0.2773 (OUTLIER) cc_final: 0.0757 (pt0) REVERT: n 108 MET cc_start: 0.3053 (tmm) cc_final: 0.1228 (mtt) REVERT: n 183 GLU cc_start: 0.3582 (pm20) cc_final: 0.3204 (tt0) REVERT: n 224 ILE cc_start: 0.3694 (mm) cc_final: 0.3366 (pt) REVERT: C 187 GLU cc_start: 0.4885 (OUTLIER) cc_final: 0.3784 (mm-30) REVERT: C 225 VAL cc_start: 0.2452 (OUTLIER) cc_final: 0.2144 (p) outliers start: 348 outliers final: 265 residues processed: 1404 average time/residue: 0.9452 time to fit residues: 2258.6164 Evaluate side-chains 1440 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1143 time to evaluate : 6.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain N residue 61 LYS Chi-restraints excluded: chain N residue 67 LYS Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 171 GLU Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain O residue 17 ARG Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 147 GLN Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain S residue 195 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 110 ASP Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 80 ILE Chi-restraints excluded: chain V residue 86 VAL Chi-restraints excluded: chain V residue 102 MET Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 115 LEU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 132 GLU Chi-restraints excluded: chain V residue 176 ASP Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain X residue 12 LYS Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 192 LYS Chi-restraints excluded: chain X residue 198 GLU Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 158 THR Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Y residue 232 LYS Chi-restraints excluded: chain Z residue 44 LYS Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 76 ARG Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain Z residue 142 THR Chi-restraints excluded: chain 0 residue 89 VAL Chi-restraints excluded: chain 0 residue 108 ASP Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 131 CYS Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 161 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 20 MET Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 106 THR Chi-restraints excluded: chain 4 residue 76 CYS Chi-restraints excluded: chain 4 residue 81 LEU Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 94 HIS Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 192 ILE Chi-restraints excluded: chain 5 residue 222 VAL Chi-restraints excluded: chain 5 residue 232 THR Chi-restraints excluded: chain 5 residue 262 ILE Chi-restraints excluded: chain 5 residue 320 SER Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 5 residue 409 GLU Chi-restraints excluded: chain 6 residue 150 ARG Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 215 THR Chi-restraints excluded: chain 6 residue 233 LEU Chi-restraints excluded: chain 6 residue 291 TYR Chi-restraints excluded: chain 6 residue 298 PHE Chi-restraints excluded: chain 6 residue 302 ASP Chi-restraints excluded: chain 6 residue 310 THR Chi-restraints excluded: chain 6 residue 321 CYS Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 40 LEU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 7 residue 73 THR Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 7 residue 105 LEU Chi-restraints excluded: chain 7 residue 120 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 172 VAL Chi-restraints excluded: chain 7 residue 175 ILE Chi-restraints excluded: chain 7 residue 183 VAL Chi-restraints excluded: chain 7 residue 219 LEU Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 253 LYS Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 107 THR Chi-restraints excluded: chain 8 residue 111 THR Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 133 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 24 GLN Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain c residue 62 GLU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 280 LEU Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain d residue 147 GLU Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 172 MET Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 214 VAL Chi-restraints excluded: chain d residue 226 ASP Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 288 LYS Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 237 LEU Chi-restraints excluded: chain f residue 101 THR Chi-restraints excluded: chain f residue 110 VAL Chi-restraints excluded: chain f residue 152 THR Chi-restraints excluded: chain f residue 190 THR Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 122 ARG Chi-restraints excluded: chain h residue 156 TRP Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 43 LEU Chi-restraints excluded: chain k residue 13 VAL Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 67 LEU Chi-restraints excluded: chain o residue 16 GLN Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain o residue 82 PHE Chi-restraints excluded: chain p residue 52 SER Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 149 ASP Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain r residue 147 LEU Chi-restraints excluded: chain r residue 186 CYS Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 185 VAL Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 232 GLN Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 263 THR Chi-restraints excluded: chain s residue 352 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 410 VAL Chi-restraints excluded: chain s residue 411 LYS Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 193 LEU Chi-restraints excluded: chain v residue 9 VAL Chi-restraints excluded: chain w residue 100 VAL Chi-restraints excluded: chain w residue 123 GLU Chi-restraints excluded: chain w residue 142 GLN Chi-restraints excluded: chain n residue 43 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 233 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 599 optimal weight: 0.8980 chunk 386 optimal weight: 1.9990 chunk 578 optimal weight: 0.4980 chunk 291 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 615 optimal weight: 8.9990 chunk 659 optimal weight: 0.4980 chunk 478 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 761 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 63 GLN F 74 GLN F 257 GLN I 61 HIS K 94 GLN ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 198 GLN M 219 ASN N 138 HIS ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 158 GLN S 118 ASN ** X 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 147 GLN 0 118 GLN 0 140 GLN 1 35 ASN ** 4 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 338 GLN 5 343 GLN ** 5 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 84 ASN ** 7 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 ASN o 91 GLN p 184 ASN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 239 ASN ** n 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 111955 Z= 0.185 Angle : 0.564 14.107 159485 Z= 0.286 Chirality : 0.038 0.294 18862 Planarity : 0.004 0.059 14202 Dihedral : 21.221 179.557 34908 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.28 % Favored : 95.68 % Rotamer: Outliers : 4.12 % Allowed : 20.64 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.01 % 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: -0.75 (0.09), residues: 8383 helix: 0.14 (0.10), residues: 2765 sheet: -0.96 (0.14), residues: 1153 loop : -0.71 (0.09), residues: 4465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP X 9 HIS 0.010 0.001 HIS 6 307 PHE 0.015 0.001 PHE 5 411 TYR 0.022 0.001 TYR e 84 ARG 0.015 0.000 ARG s 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1516 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1211 time to evaluate : 7.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 194 ASN cc_start: 0.8470 (p0) cc_final: 0.8197 (p0) REVERT: H 64 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7317 (pt) REVERT: I 90 PHE cc_start: 0.5026 (OUTLIER) cc_final: 0.3331 (m-10) REVERT: K 25 MET cc_start: 0.7610 (mmm) cc_final: 0.6960 (mmt) REVERT: K 55 ASP cc_start: 0.6995 (m-30) cc_final: 0.6489 (m-30) REVERT: L 128 ARG cc_start: 0.5256 (mpt-90) cc_final: 0.5032 (mtt90) REVERT: M 54 LYS cc_start: 0.6644 (mttp) cc_final: 0.5286 (pttm) REVERT: M 62 ARG cc_start: 0.7834 (mtm180) cc_final: 0.7616 (mtt180) REVERT: M 118 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8097 (mp) REVERT: M 210 LEU cc_start: 0.9155 (mt) cc_final: 0.8876 (mt) REVERT: N 105 MET cc_start: 0.8360 (mtm) cc_final: 0.8079 (mtm) REVERT: N 233 TYR cc_start: 0.7759 (m-80) cc_final: 0.7072 (m-80) REVERT: P 58 LEU cc_start: 0.8188 (mt) cc_final: 0.7805 (mt) REVERT: R 44 ARG cc_start: 0.8124 (mtt90) cc_final: 0.7644 (mtt90) REVERT: R 147 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7252 (mm-40) REVERT: S 181 LYS cc_start: 0.8748 (ttpt) cc_final: 0.8310 (tttm) REVERT: S 195 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8277 (mp) REVERT: T 180 GLU cc_start: 0.7042 (tt0) cc_final: 0.6827 (tt0) REVERT: U 28 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7921 (pt) REVERT: V 172 ASP cc_start: 0.6628 (m-30) cc_final: 0.6376 (m-30) REVERT: V 200 GLU cc_start: 0.5806 (mm-30) cc_final: 0.5307 (mm-30) REVERT: X 99 LYS cc_start: 0.8485 (ttmm) cc_final: 0.8240 (tttp) REVERT: Y 69 ASP cc_start: 0.6184 (OUTLIER) cc_final: 0.5707 (p0) REVERT: Y 137 ASP cc_start: 0.6678 (t0) cc_final: 0.6351 (t0) REVERT: Y 232 LYS cc_start: 0.7692 (mmtt) cc_final: 0.7106 (mmtm) REVERT: Z 47 GLN cc_start: 0.7103 (mt0) cc_final: 0.6847 (mt0) REVERT: Z 98 GLN cc_start: 0.7645 (tp-100) cc_final: 0.7346 (tp-100) REVERT: Z 136 ASN cc_start: 0.7427 (m-40) cc_final: 0.7138 (m110) REVERT: 1 20 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7475 (mtm) REVERT: 5 95 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6787 (mp0) REVERT: 5 246 GLU cc_start: 0.5413 (mm-30) cc_final: 0.5130 (tp30) REVERT: 5 355 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7979 (tp) REVERT: 6 136 ARG cc_start: 0.7064 (tpt-90) cc_final: 0.6731 (ttp80) REVERT: 6 155 TYR cc_start: 0.8443 (m-80) cc_final: 0.7969 (m-80) REVERT: 6 298 PHE cc_start: 0.5991 (OUTLIER) cc_final: 0.5610 (p90) REVERT: 6 309 GLU cc_start: 0.4523 (OUTLIER) cc_final: 0.3455 (mp0) REVERT: 7 81 MET cc_start: 0.7436 (mmm) cc_final: 0.7126 (mmt) REVERT: 7 143 TRP cc_start: 0.8549 (OUTLIER) cc_final: 0.6593 (m-90) REVERT: 7 253 LYS cc_start: 0.6499 (OUTLIER) cc_final: 0.6243 (mttm) REVERT: 8 140 LEU cc_start: 0.5181 (tp) cc_final: 0.4735 (tp) REVERT: a 111 GLN cc_start: 0.8191 (tt0) cc_final: 0.7806 (tt0) REVERT: b 24 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7675 (tt0) REVERT: c 62 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: c 227 GLU cc_start: 0.7145 (mp0) cc_final: 0.6645 (mp0) REVERT: c 240 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7577 (mp) REVERT: d 189 LEU cc_start: 0.6392 (mt) cc_final: 0.6183 (mt) REVERT: d 215 ARG cc_start: 0.6860 (ttt-90) cc_final: 0.6570 (ttt90) REVERT: d 232 MET cc_start: 0.7635 (ptp) cc_final: 0.7134 (ptp) REVERT: d 261 MET cc_start: 0.8514 (ttm) cc_final: 0.8221 (ttp) REVERT: d 281 MET cc_start: 0.8194 (tmm) cc_final: 0.7878 (ttp) REVERT: i 68 LYS cc_start: 0.8454 (mtpp) cc_final: 0.8245 (mtpt) REVERT: m 45 ARG cc_start: 0.5135 (mtt180) cc_final: 0.4691 (mmt-90) REVERT: p 186 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.6174 (mp0) REVERT: q 125 MET cc_start: 0.8066 (mmm) cc_final: 0.7748 (mmm) REVERT: r 89 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7656 (mt) REVERT: r 114 LYS cc_start: 0.8164 (mttt) cc_final: 0.7907 (mttp) REVERT: s 91 TYR cc_start: 0.8427 (m-80) cc_final: 0.7976 (m-80) REVERT: u 96 MET cc_start: 0.2605 (tpp) cc_final: 0.1707 (ptm) REVERT: n 1 PRO cc_start: 0.3289 (Cg_endo) cc_final: 0.3026 (Cg_exo) REVERT: n 108 MET cc_start: 0.3045 (tmm) cc_final: 0.1265 (mtt) REVERT: n 183 GLU cc_start: 0.3621 (pm20) cc_final: 0.3291 (tt0) REVERT: C 225 VAL cc_start: 0.2551 (OUTLIER) cc_final: 0.2254 (p) outliers start: 305 outliers final: 236 residues processed: 1417 average time/residue: 0.9673 time to fit residues: 2324.8972 Evaluate side-chains 1424 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1169 time to evaluate : 7.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 90 PHE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain N residue 61 LYS Chi-restraints excluded: chain N residue 67 LYS Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 171 GLU Chi-restraints excluded: chain O residue 17 ARG Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 147 GLN Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain S residue 195 ILE Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 80 ILE Chi-restraints excluded: chain V residue 92 ASN Chi-restraints excluded: chain V residue 115 LEU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 132 GLU Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 192 LYS Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 158 THR Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Z residue 44 LYS Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain Z residue 142 THR Chi-restraints excluded: chain 0 residue 108 ASP Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 131 CYS Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 161 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 20 MET Chi-restraints excluded: chain 1 residue 55 LEU Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 106 THR Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 4 residue 76 CYS Chi-restraints excluded: chain 4 residue 81 LEU Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 192 ILE Chi-restraints excluded: chain 5 residue 222 VAL Chi-restraints excluded: chain 5 residue 232 THR Chi-restraints excluded: chain 5 residue 320 SER Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 5 residue 409 GLU Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 215 THR Chi-restraints excluded: chain 6 residue 233 LEU Chi-restraints excluded: chain 6 residue 251 THR Chi-restraints excluded: chain 6 residue 291 TYR Chi-restraints excluded: chain 6 residue 298 PHE Chi-restraints excluded: chain 6 residue 302 ASP Chi-restraints excluded: chain 6 residue 309 GLU Chi-restraints excluded: chain 6 residue 321 CYS Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 40 LEU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 7 residue 73 THR Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 7 residue 120 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 175 ILE Chi-restraints excluded: chain 7 residue 183 VAL Chi-restraints excluded: chain 7 residue 219 LEU Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 253 LYS Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 107 THR Chi-restraints excluded: chain 8 residue 111 THR Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 133 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 24 GLN Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain c residue 62 GLU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain d residue 147 GLU Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 214 VAL Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain f residue 110 VAL Chi-restraints excluded: chain f residue 152 THR Chi-restraints excluded: chain f residue 190 THR Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 156 TRP Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 43 LEU Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 67 LEU Chi-restraints excluded: chain o residue 16 GLN Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain o residue 82 PHE Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain p residue 122 THR Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 149 ASP Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain r residue 147 LEU Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 186 CYS Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 263 THR Chi-restraints excluded: chain s residue 352 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 410 VAL Chi-restraints excluded: chain s residue 411 LYS Chi-restraints excluded: chain s residue 425 LEU Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 193 LEU Chi-restraints excluded: chain v residue 9 VAL Chi-restraints excluded: chain w residue 123 GLU Chi-restraints excluded: chain n residue 43 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 233 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 881 optimal weight: 3.9990 chunk 927 optimal weight: 10.0000 chunk 846 optimal weight: 3.9990 chunk 902 optimal weight: 5.9990 chunk 543 optimal weight: 2.9990 chunk 393 optimal weight: 0.0470 chunk 708 optimal weight: 0.9990 chunk 277 optimal weight: 0.6980 chunk 815 optimal weight: 9.9990 chunk 853 optimal weight: 3.9990 chunk 899 optimal weight: 5.9990 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 63 GLN F 74 GLN F 257 GLN I 61 HIS I 151 ASN K 94 GLN ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 142 GLN M 198 GLN N 178 GLN O 112 ASN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 158 GLN S 118 ASN T 133 ASN X 15 GLN ** X 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 147 GLN 0 106 ASN 0 140 GLN ** 4 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 HIS ** 5 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 134 ASN c 48 GLN ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 153 HIS ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 ASN o 91 GLN p 184 ASN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 111955 Z= 0.340 Angle : 0.657 15.002 159485 Z= 0.331 Chirality : 0.043 0.371 18862 Planarity : 0.005 0.080 14202 Dihedral : 21.285 179.951 34908 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.20 % Favored : 94.76 % Rotamer: Outliers : 4.49 % Allowed : 20.48 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.01 % 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: -0.90 (0.09), residues: 8383 helix: 0.03 (0.10), residues: 2750 sheet: -1.06 (0.14), residues: 1187 loop : -0.79 (0.09), residues: 4446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP S 106 HIS 0.014 0.001 HIS 6 307 PHE 0.019 0.002 PHE U 24 TYR 0.024 0.002 TYR D 206 ARG 0.016 0.001 ARG s 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 1155 time to evaluate : 6.380 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: D 172 MET cc_start: 0.3620 (mmp) cc_final: 0.3401 (mmt) REVERT: D 194 ASN cc_start: 0.8428 (p0) cc_final: 0.8107 (p0) REVERT: F 292 ASP cc_start: 0.7463 (p0) cc_final: 0.6966 (p0) REVERT: H 64 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7552 (pt) REVERT: I 90 PHE cc_start: 0.4934 (OUTLIER) cc_final: 0.3194 (m-10) REVERT: K 25 MET cc_start: 0.7654 (mmm) cc_final: 0.7017 (mmt) REVERT: L 128 ARG cc_start: 0.5357 (mpt-90) cc_final: 0.5128 (mtt90) REVERT: M 54 LYS cc_start: 0.6809 (mttp) cc_final: 0.5427 (pttm) REVERT: M 62 ARG cc_start: 0.7945 (mtm180) cc_final: 0.7699 (mtt180) REVERT: M 118 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8097 (mp) REVERT: N 105 MET cc_start: 0.8447 (mtm) cc_final: 0.8166 (mtm) REVERT: P 58 LEU cc_start: 0.8393 (mt) cc_final: 0.8043 (mt) REVERT: Q 175 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7322 (pt0) REVERT: R 10 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.7747 (mt) REVERT: R 147 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7342 (mm-40) REVERT: S 63 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6608 (mm-30) REVERT: S 119 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6418 (tt0) REVERT: S 181 LYS cc_start: 0.8909 (ttpt) cc_final: 0.8360 (tttm) REVERT: T 142 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8329 (mt) REVERT: T 180 GLU cc_start: 0.7244 (tt0) cc_final: 0.6968 (tt0) REVERT: U 28 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8111 (pt) REVERT: V 172 ASP cc_start: 0.6834 (m-30) cc_final: 0.6546 (m-30) REVERT: X 44 ARG cc_start: 0.7777 (ptp-170) cc_final: 0.7473 (mtm110) REVERT: X 99 LYS cc_start: 0.8374 (ttmm) cc_final: 0.8105 (tttp) REVERT: X 198 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6552 (tt0) REVERT: Y 69 ASP cc_start: 0.6416 (OUTLIER) cc_final: 0.5833 (p0) REVERT: Y 137 ASP cc_start: 0.6595 (t0) cc_final: 0.6306 (t0) REVERT: Y 190 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7701 (pt) REVERT: Y 232 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7158 (mmtm) REVERT: Z 47 GLN cc_start: 0.7208 (mt0) cc_final: 0.6999 (mt0) REVERT: Z 76 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8274 (mtp85) REVERT: Z 98 GLN cc_start: 0.7664 (tp-100) cc_final: 0.7339 (tp-100) REVERT: Z 136 ASN cc_start: 0.7435 (m-40) cc_final: 0.7155 (m110) REVERT: 1 20 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7662 (mtm) REVERT: 5 95 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6921 (mp0) REVERT: 5 246 GLU cc_start: 0.5737 (mm-30) cc_final: 0.5292 (tp30) REVERT: 5 355 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8014 (tp) REVERT: 6 150 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.6882 (ptp90) REVERT: 6 155 TYR cc_start: 0.8445 (m-80) cc_final: 0.8012 (m-80) REVERT: 6 298 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5687 (p90) REVERT: 6 309 GLU cc_start: 0.4674 (OUTLIER) cc_final: 0.3567 (mp0) REVERT: 7 81 MET cc_start: 0.7546 (mmm) cc_final: 0.7221 (mmt) REVERT: 7 143 TRP cc_start: 0.8618 (OUTLIER) cc_final: 0.6473 (m-90) REVERT: 7 253 LYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6330 (mttm) REVERT: 8 140 LEU cc_start: 0.5146 (OUTLIER) cc_final: 0.4660 (tp) REVERT: a 111 GLN cc_start: 0.8186 (tt0) cc_final: 0.7782 (tt0) REVERT: b 24 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: c 62 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6545 (mp0) REVERT: c 227 GLU cc_start: 0.7647 (mp0) cc_final: 0.7178 (mp0) REVERT: c 240 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7680 (mp) REVERT: d 261 MET cc_start: 0.8570 (ttm) cc_final: 0.8268 (ttp) REVERT: d 281 MET cc_start: 0.8095 (tmm) cc_final: 0.7849 (ttp) REVERT: f 60 LYS cc_start: 0.6432 (pttt) cc_final: 0.5900 (ptmt) REVERT: h 122 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6049 (mmt180) REVERT: i 68 LYS cc_start: 0.8496 (mtpp) cc_final: 0.8227 (mtpt) REVERT: m 45 ARG cc_start: 0.5151 (mtt180) cc_final: 0.4669 (mmt-90) REVERT: o 45 ASN cc_start: 0.8288 (m-40) cc_final: 0.8055 (m110) REVERT: p 186 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5771 (mp0) REVERT: q 125 MET cc_start: 0.7942 (mmm) cc_final: 0.7594 (mmm) REVERT: r 69 GLN cc_start: 0.7132 (mm110) cc_final: 0.6789 (mm110) REVERT: r 89 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7733 (mt) REVERT: r 114 LYS cc_start: 0.8151 (mttt) cc_final: 0.7874 (mttp) REVERT: s 91 TYR cc_start: 0.8511 (m-80) cc_final: 0.7940 (m-80) REVERT: s 232 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: s 411 LYS cc_start: 0.6855 (OUTLIER) cc_final: 0.6101 (ptpp) REVERT: n 1 PRO cc_start: 0.3446 (Cg_endo) cc_final: 0.3222 (Cg_exo) REVERT: n 108 MET cc_start: 0.3051 (tmm) cc_final: 0.1288 (mtt) REVERT: n 183 GLU cc_start: 0.3774 (pm20) cc_final: 0.3371 (tt0) REVERT: n 224 ILE cc_start: 0.3812 (mm) cc_final: 0.3452 (pt) REVERT: C 225 VAL cc_start: 0.2551 (OUTLIER) cc_final: 0.2289 (p) outliers start: 333 outliers final: 267 residues processed: 1387 average time/residue: 0.9743 time to fit residues: 2290.5244 Evaluate side-chains 1433 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1135 time to evaluate : 7.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain N residue 61 LYS Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 171 GLU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 175 GLN Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 147 GLN Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 86 VAL Chi-restraints excluded: chain V residue 92 ASN Chi-restraints excluded: chain V residue 115 LEU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 176 ASP Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 192 LYS Chi-restraints excluded: chain X residue 198 GLU Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 158 THR Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Y residue 232 LYS Chi-restraints excluded: chain Z residue 44 LYS Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 76 ARG Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain Z residue 142 THR Chi-restraints excluded: chain 0 residue 89 VAL Chi-restraints excluded: chain 0 residue 108 ASP Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 131 CYS Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 161 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 20 MET Chi-restraints excluded: chain 1 residue 47 ASP Chi-restraints excluded: chain 1 residue 55 LEU Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 106 THR Chi-restraints excluded: chain 3 residue 112 ASP Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 4 residue 76 CYS Chi-restraints excluded: chain 4 residue 81 LEU Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 192 ILE Chi-restraints excluded: chain 5 residue 222 VAL Chi-restraints excluded: chain 5 residue 232 THR Chi-restraints excluded: chain 5 residue 320 SER Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 5 residue 409 GLU Chi-restraints excluded: chain 6 residue 150 ARG Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 215 THR Chi-restraints excluded: chain 6 residue 233 LEU Chi-restraints excluded: chain 6 residue 298 PHE Chi-restraints excluded: chain 6 residue 302 ASP Chi-restraints excluded: chain 6 residue 309 GLU Chi-restraints excluded: chain 6 residue 310 THR Chi-restraints excluded: chain 6 residue 321 CYS Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 40 LEU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 7 residue 73 THR Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 7 residue 120 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 172 VAL Chi-restraints excluded: chain 7 residue 175 ILE Chi-restraints excluded: chain 7 residue 183 VAL Chi-restraints excluded: chain 7 residue 219 LEU Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 253 LYS Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 107 THR Chi-restraints excluded: chain 8 residue 111 THR Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain 8 residue 160 GLU Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 133 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 24 GLN Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain c residue 62 GLU Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain d residue 147 GLU Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 172 MET Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 211 GLN Chi-restraints excluded: chain d residue 214 VAL Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 288 LYS Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 143 LYS Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain f residue 110 VAL Chi-restraints excluded: chain f residue 152 THR Chi-restraints excluded: chain f residue 190 THR Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 156 GLU Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 122 ARG Chi-restraints excluded: chain h residue 156 TRP Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 43 LEU Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 67 LEU Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain o residue 16 GLN Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain o residue 82 PHE Chi-restraints excluded: chain p residue 52 SER Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain p residue 122 THR Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 149 ASP Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain r residue 147 LEU Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 186 CYS Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 185 VAL Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 232 GLN Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 263 THR Chi-restraints excluded: chain s residue 352 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 410 VAL Chi-restraints excluded: chain s residue 411 LYS Chi-restraints excluded: chain s residue 425 LEU Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 193 LEU Chi-restraints excluded: chain v residue 9 VAL Chi-restraints excluded: chain w residue 123 GLU Chi-restraints excluded: chain n residue 43 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 238 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 592 optimal weight: 0.9980 chunk 954 optimal weight: 4.9990 chunk 582 optimal weight: 0.8980 chunk 452 optimal weight: 0.0980 chunk 663 optimal weight: 0.0770 chunk 1001 optimal weight: 10.0000 chunk 921 optimal weight: 2.9990 chunk 797 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 615 optimal weight: 10.0000 chunk 488 optimal weight: 0.0020 overall best weight: 0.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 74 GLN F 257 GLN I 61 HIS K 94 GLN ** L 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 ASN L 142 GLN M 198 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN X 15 GLN X 53 ASN Y 147 GLN 0 106 ASN 0 140 GLN ** 4 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 353 HIS 7 232 HIS ** 7 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 211 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 184 ASN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 111955 Z= 0.156 Angle : 0.552 14.106 159485 Z= 0.280 Chirality : 0.037 0.267 18862 Planarity : 0.004 0.061 14202 Dihedral : 21.159 179.819 34908 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 3.37 % Allowed : 21.73 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.01 % 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: -0.55 (0.09), residues: 8383 helix: 0.37 (0.10), residues: 2760 sheet: -0.86 (0.14), residues: 1139 loop : -0.62 (0.09), residues: 4484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP X 9 HIS 0.011 0.001 HIS 6 307 PHE 0.016 0.001 PHE C 193 TYR 0.022 0.001 TYR e 84 ARG 0.018 0.000 ARG 7 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16766 Ramachandran restraints generated. 8383 Oldfield, 0 Emsley, 8383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1471 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1222 time to evaluate : 6.434 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: D 194 ASN cc_start: 0.8473 (p0) cc_final: 0.8162 (p0) REVERT: H 64 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7418 (mp) REVERT: I 90 PHE cc_start: 0.4767 (OUTLIER) cc_final: 0.3002 (m-10) REVERT: K 25 MET cc_start: 0.7619 (mmm) cc_final: 0.6970 (mmt) REVERT: K 55 ASP cc_start: 0.6984 (m-30) cc_final: 0.6486 (m-30) REVERT: L 128 ARG cc_start: 0.5194 (mpt-90) cc_final: 0.4970 (mtt90) REVERT: M 54 LYS cc_start: 0.6588 (mttp) cc_final: 0.5266 (pttm) REVERT: M 62 ARG cc_start: 0.7813 (mtm180) cc_final: 0.7605 (mtt180) REVERT: M 210 LEU cc_start: 0.9148 (mt) cc_final: 0.8882 (mt) REVERT: M 246 ASP cc_start: 0.7085 (t0) cc_final: 0.6835 (t0) REVERT: N 61 LYS cc_start: 0.6840 (OUTLIER) cc_final: 0.6480 (mttm) REVERT: N 105 MET cc_start: 0.8353 (mtm) cc_final: 0.8070 (mtm) REVERT: N 111 ARG cc_start: 0.7288 (mtm110) cc_final: 0.6847 (mtm-85) REVERT: N 150 TYR cc_start: 0.8810 (m-80) cc_final: 0.8348 (m-80) REVERT: N 233 TYR cc_start: 0.7729 (m-80) cc_final: 0.7040 (m-80) REVERT: O 100 GLN cc_start: 0.7022 (pt0) cc_final: 0.6698 (pt0) REVERT: O 107 MET cc_start: 0.7548 (ttt) cc_final: 0.7129 (ttt) REVERT: P 58 LEU cc_start: 0.8158 (mt) cc_final: 0.7786 (mt) REVERT: Q 152 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8101 (ttm-80) REVERT: R 44 ARG cc_start: 0.8083 (mtt90) cc_final: 0.7565 (mtt90) REVERT: S 63 GLU cc_start: 0.6664 (mm-30) cc_final: 0.6381 (mm-30) REVERT: S 181 LYS cc_start: 0.8756 (ttpt) cc_final: 0.8370 (ttpt) REVERT: T 180 GLU cc_start: 0.6984 (tt0) cc_final: 0.6773 (tt0) REVERT: U 28 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7907 (pt) REVERT: V 63 GLU cc_start: 0.6262 (tm-30) cc_final: 0.5885 (tt0) REVERT: V 172 ASP cc_start: 0.6581 (m-30) cc_final: 0.6328 (m-30) REVERT: V 200 GLU cc_start: 0.5682 (mm-30) cc_final: 0.5284 (mm-30) REVERT: X 99 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8271 (tttp) REVERT: X 198 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6408 (tt0) REVERT: Y 69 ASP cc_start: 0.6120 (OUTLIER) cc_final: 0.5679 (p0) REVERT: Y 137 ASP cc_start: 0.6608 (t0) cc_final: 0.6298 (t0) REVERT: Y 232 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7096 (mmtm) REVERT: Z 47 GLN cc_start: 0.7109 (mt0) cc_final: 0.6867 (mt0) REVERT: Z 98 GLN cc_start: 0.7630 (tp-100) cc_final: 0.7342 (tp-100) REVERT: Z 136 ASN cc_start: 0.7420 (m-40) cc_final: 0.7128 (m110) REVERT: 1 20 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7390 (mtm) REVERT: 5 95 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6702 (mp0) REVERT: 5 246 GLU cc_start: 0.5434 (mm-30) cc_final: 0.5124 (tp30) REVERT: 5 355 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7953 (tp) REVERT: 6 136 ARG cc_start: 0.7127 (tpt-90) cc_final: 0.6772 (ttp80) REVERT: 6 155 TYR cc_start: 0.8440 (m-80) cc_final: 0.7989 (m-80) REVERT: 6 263 SER cc_start: 0.8530 (p) cc_final: 0.8305 (p) REVERT: 6 298 PHE cc_start: 0.5647 (OUTLIER) cc_final: 0.5317 (p90) REVERT: 6 377 TYR cc_start: 0.8491 (m-80) cc_final: 0.8124 (m-80) REVERT: 7 81 MET cc_start: 0.7457 (mmm) cc_final: 0.7165 (mmt) REVERT: 7 143 TRP cc_start: 0.8533 (OUTLIER) cc_final: 0.6591 (m-90) REVERT: 7 253 LYS cc_start: 0.6494 (OUTLIER) cc_final: 0.6264 (mttm) REVERT: 8 140 LEU cc_start: 0.5177 (tp) cc_final: 0.4761 (tp) REVERT: a 111 GLN cc_start: 0.8179 (tt0) cc_final: 0.7797 (tt0) REVERT: b 24 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: c 62 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: d 215 ARG cc_start: 0.6853 (ttt-90) cc_final: 0.6564 (ttt90) REVERT: d 261 MET cc_start: 0.8465 (ttm) cc_final: 0.8205 (ttp) REVERT: d 281 MET cc_start: 0.8172 (tmm) cc_final: 0.7855 (ttp) REVERT: g 148 ARG cc_start: 0.7476 (ttm-80) cc_final: 0.7198 (ttt180) REVERT: i 68 LYS cc_start: 0.8435 (mtpp) cc_final: 0.8177 (mtpt) REVERT: m 45 ARG cc_start: 0.5117 (mtt180) cc_final: 0.4651 (mmt-90) REVERT: p 186 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.6174 (mp0) REVERT: q 125 MET cc_start: 0.8123 (mmm) cc_final: 0.7817 (mmm) REVERT: r 114 LYS cc_start: 0.8133 (mttt) cc_final: 0.7900 (mttp) REVERT: s 91 TYR cc_start: 0.8404 (m-80) cc_final: 0.7949 (m-80) REVERT: s 179 GLN cc_start: 0.7078 (mm-40) cc_final: 0.6803 (mm110) REVERT: u 96 MET cc_start: 0.2371 (tpp) cc_final: 0.1623 (ptm) REVERT: n 1 PRO cc_start: 0.3465 (Cg_endo) cc_final: 0.3184 (Cg_exo) REVERT: n 108 MET cc_start: 0.3247 (tmm) cc_final: 0.1453 (mtt) REVERT: n 183 GLU cc_start: 0.3615 (pm20) cc_final: 0.3277 (tt0) REVERT: C 225 VAL cc_start: 0.2484 (OUTLIER) cc_final: 0.2221 (p) outliers start: 249 outliers final: 202 residues processed: 1394 average time/residue: 0.9740 time to fit residues: 2305.7579 Evaluate side-chains 1401 residues out of total 7521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1182 time to evaluate : 7.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain N residue 61 LYS Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 171 GLU Chi-restraints excluded: chain N residue 172 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 115 LEU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 198 GLU Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain Y residue 69 ASP Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 158 THR Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Y residue 232 LYS Chi-restraints excluded: chain Z residue 44 LYS Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain 0 residue 108 ASP Chi-restraints excluded: chain 0 residue 116 LEU Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 161 THR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 20 MET Chi-restraints excluded: chain 1 residue 47 ASP Chi-restraints excluded: chain 1 residue 55 LEU Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 106 THR Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 4 residue 76 CYS Chi-restraints excluded: chain 4 residue 81 LEU Chi-restraints excluded: chain 5 residue 167 THR Chi-restraints excluded: chain 5 residue 222 VAL Chi-restraints excluded: chain 5 residue 232 THR Chi-restraints excluded: chain 5 residue 320 SER Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 409 GLU Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 215 THR Chi-restraints excluded: chain 6 residue 233 LEU Chi-restraints excluded: chain 6 residue 298 PHE Chi-restraints excluded: chain 6 residue 302 ASP Chi-restraints excluded: chain 6 residue 310 THR Chi-restraints excluded: chain 6 residue 321 CYS Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 40 LEU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 7 residue 73 THR Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 7 residue 120 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 175 ILE Chi-restraints excluded: chain 7 residue 183 VAL Chi-restraints excluded: chain 7 residue 219 LEU Chi-restraints excluded: chain 7 residue 221 VAL Chi-restraints excluded: chain 7 residue 253 LYS Chi-restraints excluded: chain 7 residue 314 ASP Chi-restraints excluded: chain 8 residue 107 THR Chi-restraints excluded: chain 8 residue 111 THR Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 24 GLN Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain c residue 62 GLU Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 308 THR Chi-restraints excluded: chain d residue 147 GLU Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 211 GLN Chi-restraints excluded: chain d residue 214 VAL Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain e residue 51 LEU Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain f residue 110 VAL Chi-restraints excluded: chain f residue 152 THR Chi-restraints excluded: chain f residue 190 THR Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 156 TRP Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 43 LEU Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 67 LEU Chi-restraints excluded: chain o residue 16 GLN Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain o residue 82 PHE Chi-restraints excluded: chain p residue 52 SER Chi-restraints excluded: chain p residue 122 THR Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain r residue 147 LEU Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 186 CYS Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 263 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 411 LYS Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain s residue 425 LEU Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain v residue 9 VAL Chi-restraints excluded: chain w residue 123 GLU Chi-restraints excluded: chain n residue 43 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 233 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 633 optimal weight: 0.0770 chunk 849 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 735 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 798 optimal weight: 0.5980 chunk 334 optimal weight: 0.7980 chunk 819 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 294 ASN F 63 GLN F 74 GLN F 257 GLN I 61 HIS ** L 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 142 GLN M 198 GLN N 86 ASN O 128 ASN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** T 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 147 GLN 0 106 ASN 0 140 GLN ** 4 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 232 HIS ** 7 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 127 GLN ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 134 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 211 GLN ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 ASN p 123 HIS ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.174465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.141332 restraints weight = 149360.635| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.05 r_work: 0.3212 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 111955 Z= 0.173 Angle : 0.553 14.105 159485 Z= 0.280 Chirality : 0.038 0.272 18862 Planarity : 0.004 0.069 14202 Dihedral : 21.092 179.714 34908 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.20 % Favored : 95.75 % Rotamer: Outliers : 3.20 % Allowed : 21.98 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.01 % 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: -0.44 (0.09), residues: 8383 helix: 0.48 (0.10), residues: 2765 sheet: -0.79 (0.15), residues: 1154 loop : -0.58 (0.09), residues: 4464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP N 99 HIS 0.011 0.001 HIS 6 307 PHE 0.015 0.001 PHE T 108 TYR 0.023 0.001 TYR e 84 ARG 0.016 0.000 ARG s 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34027.77 seconds wall clock time: 589 minutes 45.29 seconds (35385.29 seconds total)