Starting phenix.real_space_refine on Thu Feb 22 10:46:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oie_12927/02_2024/7oie_12927_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oie_12927/02_2024/7oie_12927.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oie_12927/02_2024/7oie_12927_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oie_12927/02_2024/7oie_12927_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oie_12927/02_2024/7oie_12927_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oie_12927/02_2024/7oie_12927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oie_12927/02_2024/7oie_12927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oie_12927/02_2024/7oie_12927_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oie_12927/02_2024/7oie_12927_updated.pdb" } resolution = 3.5 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= 0.001 sd= 0.027 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1529 5.49 5 Mg 2 5.21 5 S 285 5.16 5 C 57370 2.51 5 N 18130 2.21 5 O 22260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 116": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D ARG 277": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E ASP 69": "OD1" <-> "OD2" Residue "E ASP 126": "OD1" <-> "OD2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ASP 183": "OD1" <-> "OD2" Residue "E ASP 205": "OD1" <-> "OD2" Residue "E PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 301": "OD1" <-> "OD2" Residue "E GLU 330": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 135": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F ASP 277": "OD1" <-> "OD2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "I ARG 83": "NH1" <-> "NH2" Residue "I PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ARG 118": "NH1" <-> "NH2" Residue "K GLU 131": "OE1" <-> "OE2" Residue "K GLU 143": "OE1" <-> "OE2" Residue "K GLU 144": "OE1" <-> "OE2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "L ARG 37": "NH1" <-> "NH2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L ARG 99": "NH1" <-> "NH2" Residue "L PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 118": "NH1" <-> "NH2" Residue "L ARG 128": "NH1" <-> "NH2" Residue "L ARG 130": "NH1" <-> "NH2" Residue "L PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 111": "OD1" <-> "OD2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M ASP 146": "OD1" <-> "OD2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M GLU 208": "OE1" <-> "OE2" Residue "M TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 259": "NH1" <-> "NH2" Residue "M ASP 261": "OD1" <-> "OD2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N GLU 65": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "N PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 168": "OE1" <-> "OE2" Residue "N GLU 204": "OE1" <-> "OE2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O GLU 57": "OE1" <-> "OE2" Residue "O ASP 61": "OD1" <-> "OD2" Residue "O TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 67": "OD1" <-> "OD2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O ARG 137": "NH1" <-> "NH2" Residue "O ARG 138": "NH1" <-> "NH2" Residue "O ARG 153": "NH1" <-> "NH2" 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 GLU 65": "OE1" <-> "OE2" Residue "P ARG 75": "NH1" <-> "NH2" Residue "P ARG 80": "NH1" <-> "NH2" Residue "P GLU 91": "OE1" <-> "OE2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "P PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 156": "OD1" <-> "OD2" Residue "P GLU 167": "OE1" <-> "OE2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "Q ARG 74": "NH1" <-> "NH2" Residue "Q PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 86": "NH1" <-> "NH2" Residue "Q GLU 101": "OE1" <-> "OE2" Residue "Q TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 123": "OD1" <-> "OD2" Residue "Q ARG 143": "NH1" <-> "NH2" Residue "Q GLU 161": "OE1" <-> "OE2" Residue "Q PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 191": "NH1" <-> "NH2" Residue "Q TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 201": "OD1" <-> "OD2" Residue "Q GLU 219": "OE1" <-> "OE2" Residue "Q PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 244": "NH1" <-> "NH2" Residue "Q ARG 271": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R ARG 122": "NH1" <-> "NH2" Residue "R ARG 123": "NH1" <-> "NH2" Residue "R PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 85": "OE1" <-> "OE2" Residue "S GLU 126": "OE1" <-> "OE2" Residue "S ASP 139": "OD1" <-> "OD2" Residue "S PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "S GLU 165": "OE1" <-> "OE2" Residue "S ARG 184": "NH1" <-> "NH2" Residue "S GLU 199": "OE1" <-> "OE2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "T ASP 100": "OD1" <-> "OD2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T GLU 144": "OE1" <-> "OE2" Residue "T ARG 149": "NH1" <-> "NH2" Residue "T GLU 168": "OE1" <-> "OE2" Residue "T TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 30": "NH1" <-> "NH2" Residue "U ASP 38": "OD1" <-> "OD2" Residue "U PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 71": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U ARG 83": "NH1" <-> "NH2" Residue "U TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 143": "NH1" <-> "NH2" Residue "U PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 20": "NH1" <-> "NH2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "V ASP 69": "OD1" <-> "OD2" Residue "V ARG 96": "NH1" <-> "NH2" Residue "V TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 118": "NH1" <-> "NH2" Residue "V GLU 134": "OE1" <-> "OE2" Residue "V PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 143": "NH1" <-> "NH2" Residue "V ARG 145": "NH1" <-> "NH2" Residue "V ASP 176": "OD1" <-> "OD2" Residue "V ARG 185": "NH1" <-> "NH2" Residue "V GLU 197": "OE1" <-> "OE2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "W ARG 109": "NH1" <-> "NH2" Residue "X GLU 18": "OE1" <-> "OE2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 59": "NH1" <-> "NH2" Residue "X GLU 74": "OE1" <-> "OE2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X GLU 111": "OE1" <-> "OE2" Residue "X GLU 113": "OE1" <-> "OE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X ASP 136": "OD1" <-> "OD2" Residue "X ASP 142": "OD1" <-> "OD2" Residue "X PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 163": "NH1" <-> "NH2" Residue "X ARG 184": "NH1" <-> "NH2" Residue "X TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 189": "OD1" <-> "OD2" Residue "X GLU 193": "OE1" <-> "OE2" Residue "X GLU 198": "OE1" <-> "OE2" Residue "X GLU 200": "OE1" <-> "OE2" Residue "X GLU 210": "OE1" <-> "OE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 233": "OE1" <-> "OE2" Residue "Y GLU 65": "OE1" <-> "OE2" Residue "Y GLU 77": "OE1" <-> "OE2" Residue "Y ARG 91": "NH1" <-> "NH2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Y GLU 108": "OE1" <-> "OE2" Residue "Y ARG 109": "NH1" <-> "NH2" Residue "Y GLU 161": "OE1" <-> "OE2" Residue "Y ARG 162": "NH1" <-> "NH2" Residue "Y ARG 175": "NH1" <-> "NH2" Residue "Y ARG 196": "NH1" <-> "NH2" Residue "Y PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "Z TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 19": "NH1" <-> "NH2" Residue "1 ARG 34": "NH1" <-> "NH2" Residue "2 ARG 69": "NH1" <-> "NH2" Residue "3 TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 104": "NH1" <-> "NH2" Residue "3 ARG 116": "NH1" <-> "NH2" Residue "3 ARG 125": "NH1" <-> "NH2" Residue "3 GLU 146": "OE1" <-> "OE2" Residue "3 ARG 168": "NH1" <-> "NH2" Residue "3 ASP 182": "OD1" <-> "OD2" Residue "3 ARG 183": "NH1" <-> "NH2" Residue "4 TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 51": "OE1" <-> "OE2" Residue "5 GLU 56": "OE1" <-> "OE2" Residue "5 ASP 79": "OD1" <-> "OD2" Residue "5 ARG 80": "NH1" <-> "NH2" Residue "5 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 162": "NH1" <-> "NH2" Residue "5 GLU 169": "OE1" <-> "OE2" Residue "5 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 223": "NH1" <-> "NH2" Residue "5 GLU 244": "OE1" <-> "OE2" Residue "5 PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 267": "OE1" <-> "OE2" Residue "5 ASP 276": "OD1" <-> "OD2" Residue "5 GLU 281": "OE1" <-> "OE2" Residue "5 TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 ASP 307": "OD1" <-> "OD2" Residue "5 ARG 350": "NH1" <-> "NH2" Residue "5 PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 409": "OE1" <-> "OE2" Residue "5 PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 27": "NH1" <-> "NH2" Residue "6 ASP 41": "OD1" <-> "OD2" 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 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 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 159": "NH1" <-> "NH2" Residue "6 TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 192": "OE1" <-> "OE2" Residue "6 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 261": "NH1" <-> "NH2" Residue "6 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 296": "NH1" <-> "NH2" Residue "6 ARG 299": "NH1" <-> "NH2" Residue "6 ARG 322": "NH1" <-> "NH2" Residue "6 GLU 343": "OE1" <-> "OE2" Residue "6 ARG 364": "NH1" <-> "NH2" Residue "6 TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 51": "OE1" <-> "OE2" Residue "7 GLU 66": "OE1" <-> "OE2" Residue "7 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 132": "OD1" <-> "OD2" Residue "7 GLU 137": "OE1" <-> "OE2" Residue "7 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 168": "NH1" <-> "NH2" Residue "7 GLU 171": "OE1" <-> "OE2" Residue "7 PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 182": "OD1" <-> "OD2" Residue "7 GLU 191": "OE1" <-> "OE2" Residue "7 TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 250": "NH1" <-> "NH2" Residue "7 ARG 271": "NH1" <-> "NH2" Residue "8 ARG 137": "NH1" <-> "NH2" Residue "9 ARG 25": "NH1" <-> "NH2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 49": "NH1" <-> "NH2" Residue "9 GLU 55": "OE1" <-> "OE2" Residue "9 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 64": "OD1" <-> "OD2" Residue "9 GLU 82": "OE1" <-> "OE2" Residue "9 GLU 115": "OE1" <-> "OE2" Residue "9 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 48": "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 ARG 41": "NH1" <-> "NH2" Residue "b GLU 48": "OE1" <-> "OE2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 85": "NH1" <-> "NH2" 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 ARG 52": "NH1" <-> "NH2" Residue "c GLU 81": "OE1" <-> "OE2" Residue "c PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 142": "OE1" <-> "OE2" Residue "c GLU 163": "OE1" <-> "OE2" Residue "c GLU 183": "OE1" <-> "OE2" Residue "c ARG 216": "NH1" <-> "NH2" Residue "c GLU 243": "OE1" <-> "OE2" Residue "c PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 283": "OE1" <-> "OE2" Residue "c GLU 287": "OE1" <-> "OE2" Residue "c GLU 293": "OE1" <-> "OE2" Residue "d ARG 74": "NH1" <-> "NH2" Residue "d PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 136": "OD1" <-> "OD2" Residue "d ASP 158": "OD1" <-> "OD2" Residue "d ARG 159": "NH1" <-> "NH2" Residue "d PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 171": "OD1" <-> "OD2" Residue "d GLU 187": "OE1" <-> "OE2" Residue "d ASP 226": "OD1" <-> "OD2" Residue "d GLU 236": "OE1" <-> "OE2" Residue "d TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 180": "OE1" <-> "OE2" Residue "g ASP 43": "OD1" <-> "OD2" Residue "g ARG 90": "NH1" <-> "NH2" Residue "g ARG 105": "NH1" <-> "NH2" Residue "g GLU 114": "OE1" <-> "OE2" Residue "g GLU 142": "OE1" <-> "OE2" Residue "h ARG 69": "NH1" <-> "NH2" Residue "h GLU 92": "OE1" <-> "OE2" Residue "h ARG 116": "NH1" <-> "NH2" Residue "i ASP 45": "OD1" <-> "OD2" Residue "i ARG 46": "NH1" <-> "NH2" Residue "i GLU 72": "OE1" <-> "OE2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "i GLU 87": "OE1" <-> "OE2" Residue "i ARG 93": "NH1" <-> "NH2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ARG 28": "NH1" <-> "NH2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 65": "NH1" <-> "NH2" Residue "j ARG 66": "NH1" <-> "NH2" Residue "j GLU 71": "OE1" <-> "OE2" Residue "j PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 76": "NH1" <-> "NH2" Residue "j ARG 94": "NH1" <-> "NH2" Residue "j ARG 103": "NH1" <-> "NH2" Residue "k ARG 31": "NH1" <-> "NH2" Residue "k ARG 77": "NH1" <-> "NH2" Residue "k GLU 85": "OE1" <-> "OE2" Residue "k PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 11": "NH1" <-> "NH2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 68": "NH1" <-> "NH2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "p ASP 46": "OD1" <-> "OD2" Residue "p ASP 156": "OD1" <-> "OD2" Residue "p GLU 160": "OE1" <-> "OE2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 38": "NH1" <-> "NH2" Residue "q ASP 44": "OD1" <-> "OD2" Residue "q ARG 63": "NH1" <-> "NH2" Residue "q GLU 111": "OE1" <-> "OE2" Residue "q ARG 114": "NH1" <-> "NH2" Residue "q ARG 140": "NH1" <-> "NH2" Residue "q GLU 141": "OE1" <-> "OE2" Residue "r ASP 85": "OD1" <-> "OD2" Residue "r PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "s PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 103": "OD1" <-> "OD2" Residue "s TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 158": "NH1" <-> "NH2" Residue "s ARG 160": "NH1" <-> "NH2" Residue "s ARG 162": "NH1" <-> "NH2" 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 ARG 242": "NH1" <-> "NH2" Residue "s GLU 249": "OE1" <-> "OE2" Residue "s ASP 269": "OD1" <-> "OD2" Residue "s ARG 276": "NH1" <-> "NH2" Residue "s ASP 290": "OD1" <-> "OD2" Residue "s ARG 308": "NH1" <-> "NH2" Residue "s GLU 321": "OE1" <-> "OE2" Residue "s PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 348": "OE1" <-> "OE2" Residue "s ASP 363": "OD1" <-> "OD2" Residue "s PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 389": "NH1" <-> "NH2" Residue "s ASP 416": "OD1" <-> "OD2" Residue "u GLU 104": "OE1" <-> "OE2" Residue "u GLU 117": "OE1" <-> "OE2" Residue "u PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 160": "OE1" <-> "OE2" Residue "u ASP 171": "OD1" <-> "OD2" Residue "u TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 200": "OD1" <-> "OD2" Residue "v ARG 6": "NH1" <-> "NH2" Residue "v TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 14": "NH1" <-> "NH2" Residue "v ARG 24": "NH1" <-> "NH2" Residue "v TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 27": "OD1" <-> "OD2" Residue "v ARG 28": "NH1" <-> "NH2" Residue "v PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 47": "OD1" <-> "OD2" Residue "w ASP 91": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 99578 Number of models: 1 Model: "" Number of chains: 60 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: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1305 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 12, 'TRANS': 146} Chain breaks: 1 Chain: "U" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1154 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain breaks: 1 Chain: "V" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1575 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 16, 'TRANS': 175} Chain breaks: 1 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: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} 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: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 322 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} 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: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 836 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 9, 'TRANS': 89} 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: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 611 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 8, 'TRANS': 64} 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: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 786 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} 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: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1379 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 15, 'TRANS': 148} 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: "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: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 31265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 31265 Classifications: {'RNA': 1472} Modifications used: {'rna2p_pur': 156, 'rna2p_pyr': 109, 'rna3p_pur': 623, 'rna3p_pyr': 584} Link IDs: {'rna2p': 264, 'rna3p': 1207} Chain breaks: 13 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: "0" 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: "v" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 31967 SG CYS 0 110 164.719 85.613 175.217 1.00 17.41 S ATOM 31989 SG CYS 0 113 162.082 83.493 177.250 1.00 18.81 S ATOM 32069 SG CYS 0 123 161.303 86.749 175.505 1.00 0.64 S ATOM 32092 SG CYS 0 126 163.142 86.741 178.729 1.00 4.50 S ATOM 7322 SG CYS I 64 143.693 100.712 62.480 1.00 31.95 S ATOM 60940 SG CYS r 70 147.707 100.310 62.778 1.00 18.47 S ATOM 60961 SG CYS r 73 145.777 97.637 61.771 1.00 17.65 S ATOM 61255 SG CYS r 108 145.925 102.025 62.758 1.00 17.01 S Time building chain proxies: 37.28, per 1000 atoms: 0.37 Number of scatterers: 99578 At special positions: 0 Unit cell: (220.052, 223.304, 254.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 285 16.00 P 1529 15.00 Mg 2 11.99 O 22260 8.00 N 18130 7.00 C 57370 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 34.44 Conformation dependent library (CDL) restraints added in 8.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb=" ZN r 301 " pdb="ZN ZN r 301 " - pdb=" SG CYS I 64 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 70 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 108 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 73 " Number of angles added : 12 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15506 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 266 helices and 81 sheets defined 31.7% alpha, 11.6% beta 401 base pairs and 820 stacking pairs defined. Time for finding SS restraints: 33.93 Creating SS restraints... Processing helix chain 'D' and resid 184 through 186 No H-bonds generated for 'chain 'D' and resid 184 through 186' Processing helix chain 'D' and resid 260 through 265 removed outlier: 3.798A pdb=" N ARG D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 77 Processing helix chain 'E' and resid 154 through 156 No H-bonds generated for 'chain 'E' and resid 154 through 156' Processing helix chain 'E' and resid 159 through 168 Processing helix chain 'E' and resid 218 through 221 No H-bonds generated for 'chain 'E' and resid 218 through 221' Processing helix chain 'E' and resid 305 through 307 No H-bonds generated for 'chain 'E' and resid 305 through 307' Processing helix chain 'E' and resid 321 through 323 No H-bonds generated for 'chain 'E' and resid 321 through 323' Processing helix chain 'F' and resid 84 through 87 No H-bonds generated for 'chain 'F' and resid 84 through 87' Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 167 through 183 Processing helix chain 'F' and resid 200 through 209 Processing helix chain 'F' and resid 228 through 234 Processing helix chain 'F' and resid 245 through 247 No H-bonds generated for 'chain 'F' and resid 245 through 247' Processing helix chain 'F' and resid 263 through 272 Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'H' and resid 116 through 121 Processing helix chain 'H' and resid 136 through 145 Processing helix chain 'I' and resid 42 through 50 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 128 through 137 Proline residue: I 133 - end of helix Processing helix chain 'I' and resid 144 through 146 No H-bonds generated for 'chain 'I' and resid 144 through 146' Processing helix chain 'I' and resid 161 through 169 Processing helix chain 'I' and resid 188 through 196 Processing helix chain 'J' and resid 46 through 58 Processing helix chain 'J' and resid 88 through 94 Processing helix chain 'J' and resid 114 through 122 Processing helix chain 'J' and resid 137 through 149 Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 28 through 40 Processing helix chain 'K' and resid 70 through 74 Processing helix chain 'K' and resid 92 through 98 Processing helix chain 'K' and resid 102 through 111 Processing helix chain 'K' and resid 118 through 124 removed outlier: 3.914A pdb=" N GLU K 123 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 138 No H-bonds generated for 'chain 'K' and resid 135 through 138' Processing helix chain 'K' and resid 160 through 165 Processing helix chain 'L' and resid 125 through 127 No H-bonds generated for 'chain 'L' and resid 125 through 127' Processing helix chain 'L' and resid 135 through 138 No H-bonds generated for 'chain 'L' and resid 135 through 138' Processing helix chain 'M' and resid 11 through 17 Processing helix chain 'M' and resid 42 through 45 No H-bonds generated for 'chain 'M' and resid 42 through 45' Processing helix chain 'M' and resid 56 through 59 No H-bonds generated for 'chain 'M' and resid 56 through 59' Processing helix chain 'M' and resid 98 through 106 Processing helix chain 'M' and resid 118 through 123 Processing helix chain 'M' and resid 161 through 168 Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 191 through 194 No H-bonds generated for 'chain 'M' and resid 191 through 194' Processing helix chain 'M' and resid 208 through 214 Proline residue: M 212 - end of helix No H-bonds generated for 'chain 'M' and resid 208 through 214' Processing helix chain 'M' and resid 226 through 239 Proline residue: M 230 - end of helix Processing helix chain 'M' and resid 251 through 256 removed outlier: 4.315A pdb=" N LYS M 254 " --> pdb=" O GLU M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 295 removed outlier: 3.711A pdb=" N THR M 295 " --> pdb=" O LEU M 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 111 Processing helix chain 'N' and resid 169 through 182 removed outlier: 5.209A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 208 removed outlier: 3.655A pdb=" N GLU N 196 " --> pdb=" O ARG N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 215 through 220 Processing helix chain 'N' and resid 226 through 228 No H-bonds generated for 'chain 'N' and resid 226 through 228' Processing helix chain 'N' and resid 234 through 237 No H-bonds generated for 'chain 'N' and resid 234 through 237' Processing helix chain 'O' and resid 22 through 39 Processing helix chain 'O' and resid 46 through 63 Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 83 through 91 Proline residue: O 87 - end of helix Processing helix chain 'O' and resid 93 through 97 Processing helix chain 'O' and resid 144 through 158 Processing helix chain 'P' and resid 55 through 58 No H-bonds generated for 'chain 'P' and resid 55 through 58' Processing helix chain 'P' and resid 110 through 115 removed outlier: 4.780A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 139 Processing helix chain 'P' and resid 150 through 154 Processing helix chain 'P' and resid 156 through 168 Processing helix chain 'Q' and resid 78 through 80 No H-bonds generated for 'chain 'Q' and resid 78 through 80' Processing helix chain 'Q' and resid 89 through 105 Processing helix chain 'Q' and resid 144 through 146 No H-bonds generated for 'chain 'Q' and resid 144 through 146' Processing helix chain 'Q' and resid 188 through 191 Processing helix chain 'Q' and resid 195 through 197 No H-bonds generated for 'chain 'Q' and resid 195 through 197' Processing helix chain 'Q' and resid 245 through 248 No H-bonds generated for 'chain 'Q' and resid 245 through 248' Processing helix chain 'Q' and resid 251 through 260 removed outlier: 4.652A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 266 removed outlier: 4.023A pdb=" N GLU Q 266 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 263 through 266' Processing helix chain 'Q' and resid 277 through 289 removed outlier: 3.658A pdb=" N SER Q 289 " --> pdb=" O GLU Q 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 27 removed outlier: 4.458A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 36 Processing helix chain 'R' and resid 39 through 78 removed outlier: 4.939A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 90 Processing helix chain 'R' and resid 99 through 108 Processing helix chain 'R' and resid 110 through 132 removed outlier: 4.043A pdb=" N ALA R 131 " --> pdb=" O GLY R 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 89 removed outlier: 3.759A pdb=" N THR S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 53 through 56 Processing helix chain 'T' and resid 87 through 93 Processing helix chain 'T' and resid 99 through 105 Processing helix chain 'T' and resid 112 through 131 Processing helix chain 'T' and resid 192 through 203 Processing helix chain 'U' and resid 50 through 61 Processing helix chain 'U' and resid 127 through 134 Processing helix chain 'V' and resid 29 through 34 Processing helix chain 'V' and resid 81 through 83 No H-bonds generated for 'chain 'V' and resid 81 through 83' Processing helix chain 'V' and resid 117 through 119 No H-bonds generated for 'chain 'V' and resid 117 through 119' Processing helix chain 'V' and resid 179 through 182 No H-bonds generated for 'chain 'V' and resid 179 through 182' Processing helix chain 'V' and resid 194 through 201 Processing helix chain 'W' and resid 111 through 117 Processing helix chain 'X' and resid 8 through 17 removed outlier: 4.320A pdb=" N LYS X 12 " --> pdb=" O TRP X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 22 No H-bonds generated for 'chain 'X' and resid 20 through 22' Processing helix chain 'X' and resid 26 through 32 Processing helix chain 'X' and resid 73 through 76 Processing helix chain 'X' and resid 129 through 137 Processing helix chain 'X' and resid 141 through 147 Processing helix chain 'X' and resid 150 through 153 No H-bonds generated for 'chain 'X' and resid 150 through 153' Processing helix chain 'X' and resid 156 through 170 Processing helix chain 'X' and resid 181 through 190 Processing helix chain 'X' and resid 192 through 194 No H-bonds generated for 'chain 'X' and resid 192 through 194' Processing helix chain 'X' and resid 198 through 203 removed outlier: 3.544A pdb=" N GLU X 202 " --> pdb=" O GLU X 198 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 198 through 203' Processing helix chain 'X' and resid 208 through 219 Processing helix chain 'X' and resid 226 through 242 Processing helix chain 'Y' and resid 65 through 67 No H-bonds generated for 'chain 'Y' and resid 65 through 67' Processing helix chain 'Y' and resid 71 through 73 No H-bonds generated for 'chain 'Y' and resid 71 through 73' Processing helix chain 'Y' and resid 87 through 91 Processing helix chain 'Y' and resid 95 through 121 Processing helix chain 'Y' and resid 130 through 157 Processing helix chain 'Y' and resid 188 through 190 No H-bonds generated for 'chain 'Y' and resid 188 through 190' Processing helix chain 'Y' and resid 192 through 195 No H-bonds generated for 'chain 'Y' and resid 192 through 195' Processing helix chain 'Y' and resid 206 through 237 Processing helix chain 'Z' and resid 43 through 46 Processing helix chain 'Z' and resid 50 through 55 Processing helix chain 'Z' and resid 80 through 89 Processing helix chain 'Z' and resid 104 through 112 Processing helix chain '0' and resid 87 through 93 Processing helix chain '0' and resid 124 through 145 Processing helix chain '2' and resid 57 through 64 Processing helix chain '2' and resid 66 through 70 Processing helix chain '2' and resid 73 through 85 Processing helix chain '3' and resid 108 through 113 Processing helix chain '3' and resid 133 through 135 No H-bonds generated for 'chain '3' and resid 133 through 135' Processing helix chain '3' and resid 138 through 144 Processing helix chain '3' and resid 152 through 161 Processing helix chain '4' and resid 96 through 98 No H-bonds generated for 'chain '4' and resid 96 through 98' Processing helix chain '5' and resid 117 through 124 Processing helix chain '5' and resid 134 through 140 removed outlier: 4.470A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) Processing helix chain '5' and resid 150 through 162 Processing helix chain '5' and resid 173 through 192 Proline residue: 5 178 - end of helix removed outlier: 4.759A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) Processing helix chain '5' and resid 197 through 200 Processing helix chain '5' and resid 242 through 250 removed outlier: 4.251A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) Processing helix chain '5' and resid 306 through 329 Processing helix chain '5' and resid 408 through 419 removed outlier: 3.639A pdb=" N LEU 5 415 " --> pdb=" O ARG 5 412 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 66 Processing helix chain '6' and resid 74 through 78 Processing helix chain '6' and resid 100 through 114 Processing helix chain '6' and resid 117 through 124 Processing helix chain '6' and resid 132 through 141 Processing helix chain '6' and resid 144 through 154 Processing helix chain '6' and resid 157 through 161 Processing helix chain '6' and resid 293 through 296 No H-bonds generated for 'chain '6' and resid 293 through 296' Processing helix chain '6' and resid 300 through 305 Processing helix chain '6' and resid 325 through 333 Processing helix chain '6' and resid 363 through 369 removed outlier: 3.540A pdb=" N ARG 6 368 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR 6 369 " --> pdb=" O LEU 6 366 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 57 Processing helix chain '7' and resid 88 through 95 Processing helix chain '7' and resid 97 through 99 No H-bonds generated for 'chain '7' and resid 97 through 99' Processing helix chain '7' and resid 108 through 110 No H-bonds generated for 'chain '7' and resid 108 through 110' Processing helix chain '7' and resid 136 through 155 Processing helix chain '7' and resid 174 through 176 No H-bonds generated for 'chain '7' and resid 174 through 176' Processing helix chain '7' and resid 187 through 189 No H-bonds generated for 'chain '7' and resid 187 through 189' Processing helix chain '7' and resid 196 through 212 Processing helix chain '7' and resid 223 through 229 Processing helix chain '7' and resid 234 through 246 removed outlier: 3.771A pdb=" N SER 7 245 " --> pdb=" O GLU 7 241 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN 7 246 " --> pdb=" O GLU 7 242 " (cutoff:3.500A) Processing helix chain '7' and resid 310 through 319 Processing helix chain '8' and resid 108 through 153 Processing helix chain '8' and resid 158 through 161 No H-bonds generated for 'chain '8' and resid 158 through 161' Processing helix chain '9' and resid 28 through 33 Processing helix chain '9' and resid 88 through 104 Proline residue: 9 98 - end of helix Processing helix chain '9' and resid 114 through 116 No H-bonds generated for 'chain '9' and resid 114 through 116' Processing helix chain 'a' and resid 69 through 71 No H-bonds generated for 'chain 'a' and resid 69 through 71' Processing helix chain 'a' and resid 106 through 116 Processing helix chain 'a' and resid 120 through 122 No H-bonds generated for 'chain 'a' and resid 120 through 122' Processing helix chain 'a' and resid 128 through 131 No H-bonds generated for 'chain 'a' and resid 128 through 131' Processing helix chain 'b' and resid 41 through 49 Processing helix chain 'b' and resid 51 through 57 Processing helix chain 'b' and resid 94 through 105 Processing helix chain 'c' and resid 36 through 51 Processing helix chain 'c' and resid 60 through 62 No H-bonds generated for 'chain 'c' and resid 60 through 62' Processing helix chain 'c' and resid 68 through 79 removed outlier: 4.100A pdb=" N LEU c 79 " --> pdb=" O PHE c 75 " (cutoff:3.500A) Processing helix chain 'c' and resid 85 through 91 Processing helix chain 'c' and resid 96 through 105 Processing helix chain 'c' and resid 123 through 144 Processing helix chain 'c' and resid 150 through 160 Processing helix chain 'c' and resid 163 through 173 removed outlier: 3.601A pdb=" N LEU c 173 " --> pdb=" O VAL c 169 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 219 Proline residue: c 208 - end of helix Processing helix chain 'c' and resid 221 through 223 No H-bonds generated for 'chain 'c' and resid 221 through 223' Processing helix chain 'c' and resid 228 through 230 No H-bonds generated for 'chain 'c' and resid 228 through 230' Processing helix chain 'c' and resid 237 through 247 Processing helix chain 'c' and resid 289 through 305 Processing helix chain 'd' and resid 54 through 63 Processing helix chain 'd' and resid 119 through 129 removed outlier: 3.533A pdb=" N ASP d 127 " --> pdb=" O ARG d 123 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP d 129 " --> pdb=" O ILE d 125 " (cutoff:3.500A) Processing helix chain 'd' and resid 137 through 153 removed outlier: 3.770A pdb=" N LEU d 152 " --> pdb=" O ALA d 148 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN d 153 " --> pdb=" O HIS d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 158 through 163 Processing helix chain 'd' and resid 169 through 173 Processing helix chain 'e' and resid 65 through 80 Processing helix chain 'e' and resid 86 through 89 No H-bonds generated for 'chain 'e' and resid 86 through 89' Processing helix chain 'e' and resid 93 through 103 Processing helix chain 'e' and resid 117 through 130 Processing helix chain 'e' and resid 184 through 195 Processing helix chain 'e' and resid 259 through 263 Processing helix chain 'e' and resid 273 through 275 No H-bonds generated for 'chain 'e' and resid 273 through 275' Processing helix chain 'f' and resid 100 through 115 Processing helix chain 'f' and resid 164 through 176 Processing helix chain 'g' and resid 45 through 47 No H-bonds generated for 'chain 'g' and resid 45 through 47' Processing helix chain 'g' and resid 117 through 131 removed outlier: 3.887A 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 154 through 164 Processing helix chain 'h' and resid 66 through 77 Processing helix chain 'h' and resid 86 through 88 No H-bonds generated for 'chain 'h' and resid 86 through 88' Processing helix chain 'h' and resid 94 through 108 Processing helix chain 'h' and resid 114 through 116 No H-bonds generated for 'chain 'h' and resid 114 through 116' Processing helix chain 'h' and resid 123 through 131 Processing helix chain 'h' and resid 139 through 143 Processing helix chain 'i' and resid 49 through 52 No H-bonds generated for 'chain 'i' and resid 49 through 52' Processing helix chain 'i' and resid 70 through 73 Processing helix chain 'i' and resid 78 through 80 No H-bonds generated for 'chain 'i' and resid 78 through 80' Processing helix chain 'i' and resid 87 through 98 Processing helix chain 'i' and resid 104 through 123 Processing helix chain 'j' and resid 27 through 30 No H-bonds generated for 'chain 'j' and resid 27 through 30' Processing helix chain 'j' and resid 42 through 45 No H-bonds generated for 'chain 'j' and resid 42 through 45' Processing helix chain 'j' and resid 61 through 105 Processing helix chain 'k' and resid 28 through 36 Processing helix chain 'k' and resid 40 through 43 No H-bonds generated for 'chain 'k' and resid 40 through 43' Processing helix chain 'k' and resid 83 through 95 Processing helix chain 'l' and resid 115 through 132 Processing helix chain 'o' and resid 29 through 50 removed outlier: 4.240A pdb=" N SER o 50 " --> pdb=" O HIS o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 64 through 78 Processing helix chain 'o' and resid 89 through 98 removed outlier: 4.717A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) Processing helix chain 'p' and resid 45 through 48 No H-bonds generated for 'chain 'p' and resid 45 through 48' Processing helix chain 'p' and resid 55 through 58 Processing helix chain 'p' and resid 113 through 121 Processing helix chain 'p' and resid 124 through 126 No H-bonds generated for 'chain 'p' and resid 124 through 126' Processing helix chain 'p' and resid 143 through 162 Processing helix chain 'p' and resid 175 through 188 Processing helix chain 'q' and resid 55 through 64 Processing helix chain 'q' and resid 66 through 68 No H-bonds generated for 'chain 'q' and resid 66 through 68' Processing helix chain 'q' and resid 72 through 75 removed outlier: 3.797A pdb=" N LEU q 75 " --> pdb=" O PRO q 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 72 through 75' Processing helix chain 'q' and resid 79 through 92 Processing helix chain 'q' and resid 96 through 154 Proline residue: q 129 - end of helix Processing helix chain 'q' and resid 170 through 187 Processing helix chain 'r' and resid 71 through 75 removed outlier: 3.576A pdb=" N TRP r 75 " --> pdb=" O PRO r 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 71 through 75' Processing helix chain 'r' and resid 86 through 92 removed outlier: 4.338A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) Processing helix chain 'r' and resid 102 through 105 No H-bonds generated for 'chain 'r' and resid 102 through 105' Processing helix chain 'r' and resid 109 through 123 Processing helix chain 'r' and resid 156 through 158 No H-bonds generated for 'chain 'r' and resid 156 through 158' Processing helix chain 'r' and resid 168 through 170 No H-bonds generated for 'chain 'r' and resid 168 through 170' Processing helix chain 'r' and resid 179 through 181 No H-bonds generated for 'chain 'r' and resid 179 through 181' Processing helix chain 's' and resid 57 through 71 Processing helix chain 's' and resid 76 through 83 Processing helix chain 's' and resid 102 through 110 Processing helix chain 's' and resid 142 through 154 Processing helix chain 's' and resid 174 through 188 Processing helix chain 's' and resid 194 through 197 Processing helix chain 's' and resid 304 through 306 No H-bonds generated for 'chain 's' and resid 304 through 306' Processing helix chain 's' and resid 308 through 311 No H-bonds generated for 'chain 's' and resid 308 through 311' Processing helix chain 's' and resid 318 through 343 Processing helix chain 's' and resid 416 through 426 Processing helix chain 'u' and resid 94 through 104 Processing helix chain 'u' and resid 132 through 149 Processing helix chain 'u' and resid 182 through 188 Processing helix chain 'u' and resid 190 through 193 No H-bonds generated for 'chain 'u' and resid 190 through 193' Processing helix chain 'v' and resid 7 through 21 Processing helix chain 'v' and resid 28 through 39 Processing helix chain 'v' and resid 48 through 63 Processing helix chain 'w' and resid 76 through 88 Processing helix chain 'w' and resid 112 through 123 Processing helix chain 'w' and resid 132 through 137 removed outlier: 3.536A pdb=" N GLU w 136 " --> pdb=" O ASP w 132 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LYS w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 132 through 137' Processing helix chain 'w' and resid 141 through 151 Processing sheet with id= A, first strand: chain 'D' and resid 162 through 165 removed outlier: 6.420A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE D 139 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= C, first strand: chain 'D' and resid 233 through 237 removed outlier: 6.428A pdb=" N GLN D 227 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU D 216 " --> pdb=" O GLN D 227 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 265 through 268 removed outlier: 5.027A pdb=" N LYS E 209 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU E 296 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU E 121 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL E 119 " --> pdb=" O MET E 106 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASN E 286 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E 273 " --> pdb=" O ASN E 286 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 175 through 181 removed outlier: 6.247A pdb=" N GLY E 148 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VAL E 129 " --> pdb=" O GLY E 148 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 214 through 216 Processing sheet with id= G, first strand: chain 'F' and resid 62 through 65 Processing sheet with id= H, first strand: chain 'F' and resid 187 through 190 removed outlier: 6.500A pdb=" N LEU F 259 " --> pdb=" O HIS F 188 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N MET F 190 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU F 261 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 111 through 114 Processing sheet with id= J, first strand: chain 'H' and resid 54 through 58 removed outlier: 6.716A pdb=" N GLU H 57 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU H 82 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'I' and resid 122 through 124 Processing sheet with id= L, first strand: chain 'I' and resid 179 through 181 Processing sheet with id= M, first strand: chain 'J' and resid 110 through 113 Processing sheet with id= N, first strand: chain 'K' and resid 125 through 127 removed outlier: 6.263A pdb=" N VAL K 57 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU K 20 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU K 144 " --> pdb=" O LEU K 20 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP K 22 " --> pdb=" O GLU K 144 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'K' and resid 76 through 80 Processing sheet with id= P, first strand: chain 'L' and resid 84 through 86 Processing sheet with id= Q, first strand: chain 'M' and resid 153 through 156 removed outlier: 6.537A pdb=" N VAL M 173 " --> pdb=" O ILE M 154 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL M 156 " --> pdb=" O VAL M 173 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N THR M 175 " --> pdb=" O VAL M 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 274 through 276 Processing sheet with id= S, first strand: chain 'M' and resid 92 through 97 removed outlier: 6.731A pdb=" N LYS M 94 " --> pdb=" O TYR M 136 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU M 96 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU M 140 " --> pdb=" O LEU M 96 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'N' and resid 87 through 92 Processing sheet with id= U, first strand: chain 'N' and resid 95 through 97 Processing sheet with id= V, first strand: chain 'N' and resid 118 through 122 Processing sheet with id= W, first strand: chain 'N' and resid 129 through 132 Processing sheet with id= X, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.620A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'P' and resid 79 through 86 removed outlier: 5.933A pdb=" N HIS P 96 " --> pdb=" O VAL P 101 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL P 101 " --> pdb=" O HIS P 96 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Q' and resid 173 through 178 removed outlier: 6.717A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N LEU Q 134 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL Q 154 " --> pdb=" O LEU Q 134 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE Q 150 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'S' and resid 104 through 109 removed outlier: 3.533A pdb=" N PHE S 101 " --> pdb=" O ARG S 104 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS S 100 " --> pdb=" O VAL S 133 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL S 133 " --> pdb=" O HIS S 100 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'S' and resid 112 through 116 Processing sheet with id= AC, first strand: chain 'S' and resid 127 through 129 removed outlier: 6.691A pdb=" N THR S 159 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE S 195 " --> pdb=" O THR S 159 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'S' and resid 169 through 175 Processing sheet with id= AE, first strand: chain 'T' and resid 72 through 77 removed outlier: 6.669A pdb=" N VAL T 179 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE T 142 " --> pdb=" O VAL T 179 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'T' and resid 153 through 155 Processing sheet with id= AG, first strand: chain 'U' and resid 39 through 42 Processing sheet with id= AH, first strand: chain 'V' and resid 120 through 122 removed outlier: 7.056A pdb=" N VAL V 87 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL V 79 " --> pdb=" O TRP V 85 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP V 85 " --> pdb=" O VAL V 79 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'V' and resid 93 through 98 Processing sheet with id= AJ, first strand: chain 'V' and resid 133 through 137 removed outlier: 3.623A pdb=" N VAL V 146 " --> pdb=" O GLU V 134 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG V 136 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL V 144 " --> pdb=" O ARG V 136 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'W' and resid 81 through 83 Processing sheet with id= AL, first strand: chain 'W' and resid 95 through 103 Processing sheet with id= AM, first strand: chain 'X' and resid 50 through 52 Processing sheet with id= AN, first strand: chain 'X' and resid 86 through 91 Processing sheet with id= AO, first strand: chain 'X' and resid 110 through 116 Processing sheet with id= AP, first strand: chain 'Y' and resid 166 through 170 Processing sheet with id= AQ, first strand: chain 'Z' and resid 98 through 101 Processing sheet with id= AR, first strand: chain '0' and resid 107 through 109 Processing sheet with id= AS, first strand: chain '0' and resid 156 through 159 removed outlier: 6.277A pdb=" N ARG 0 173 " --> pdb=" O VAL 0 157 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU 0 159 " --> pdb=" O ARG 0 173 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE 0 175 " --> pdb=" O LEU 0 159 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain '1' and resid 29 through 35 Processing sheet with id= AU, first strand: chain '1' and resid 17 through 19 removed outlier: 6.537A pdb=" N ARG 1 19 " --> pdb=" O LYS 1 61 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS 1 61 " --> pdb=" O ARG 1 19 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain '3' and resid 115 through 117 Processing sheet with id= AW, first strand: chain '4' and resid 80 through 84 Processing sheet with id= AX, first strand: chain '5' and resid 266 through 268 removed outlier: 3.778A pdb=" N SER 5 207 " --> pdb=" O GLY 5 226 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain '5' and resid 126 through 130 removed outlier: 7.102A pdb=" N ASN 5 372 " --> pdb=" O LYS 5 127 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE 5 129 " --> pdb=" O ASN 5 372 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA 5 374 " --> pdb=" O ILE 5 129 " (cutoff:3.500A) removed outlier: 10.009A pdb=" N VAL 5 341 " --> pdb=" O TYR 5 287 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N HIS 5 289 " --> pdb=" O VAL 5 341 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU 5 230 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain '5' and resid 385 through 387 Processing sheet with id= BA, first strand: chain '6' and resid 203 through 205 Processing sheet with id= BB, first strand: chain '6' and resid 249 through 252 removed outlier: 7.105A pdb=" N LEU 6 236 " --> pdb=" O THR 6 251 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TRP 6 214 " --> pdb=" O ASN 6 239 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LYS 6 274 " --> pdb=" O PRO 6 313 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain '7' and resid 64 through 69 Processing sheet with id= BD, first strand: chain '7' and resid 111 through 113 removed outlier: 6.458A pdb=" N LEU 7 128 " --> pdb=" O ILE 7 104 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain '7' and resid 179 through 184 Processing sheet with id= BF, first strand: chain '7' and resid 217 through 222 Processing sheet with id= BG, first strand: chain '7' and resid 275 through 280 removed outlier: 6.571A pdb=" N LEU 7 302 " --> pdb=" O PHE 7 276 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR 7 278 " --> pdb=" O VAL 7 300 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL 7 300 " --> pdb=" O TYR 7 278 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain '9' and resid 42 through 45 Processing sheet with id= BI, first strand: chain 'a' and resid 48 through 51 Processing sheet with id= BJ, first strand: chain 'b' and resid 28 through 32 removed outlier: 6.543A pdb=" N VAL b 62 " --> pdb=" O LEU b 29 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE b 31 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR b 64 " --> pdb=" O PHE b 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= BJ Processing sheet with id= BK, first strand: chain 'b' and resid 74 through 78 Processing sheet with id= BL, first strand: chain 'c' and resid 254 through 259 removed outlier: 6.548A pdb=" N PHE c 271 " --> pdb=" O THR c 258 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'd' and resid 184 through 186 removed outlier: 5.679A pdb=" N GLU d 249 " --> pdb=" O MET d 261 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N MET d 261 " --> pdb=" O GLU d 249 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'd' and resid 193 through 198 removed outlier: 6.480A pdb=" N THR d 213 " --> pdb=" O VAL d 195 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLN d 211 " --> pdb=" O VAL d 197 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'e' and resid 175 through 177 removed outlier: 7.188A pdb=" N GLY e 228 " --> pdb=" O ARG e 46 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU e 48 " --> pdb=" O GLY e 228 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LYS e 230 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA e 50 " --> pdb=" O LYS e 230 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE e 232 " --> pdb=" O ALA e 50 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'e' and resid 161 through 164 Processing sheet with id= BQ, first strand: chain 'e' and resid 199 through 203 removed outlier: 6.178A pdb=" N LYS e 203 " --> pdb=" O LEU e 238 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU e 238 " --> pdb=" O LYS e 203 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'f' and resid 93 through 97 Processing sheet with id= BS, first strand: chain 'g' and resid 84 through 86 Processing sheet with id= BT, first strand: chain 'g' and resid 96 through 101 Processing sheet with id= BU, first strand: chain 'k' and resid 51 through 55 removed outlier: 6.344A pdb=" N VAL k 16 " --> pdb=" O ILE k 52 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ASP k 54 " --> pdb=" O VAL k 16 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL k 18 " --> pdb=" O ASP k 54 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'm' and resid 52 through 56 Processing sheet with id= BW, first strand: chain 'p' and resid 77 through 81 Processing sheet with id= BX, first strand: chain 'r' and resid 36 through 41 Processing sheet with id= BY, first strand: chain 's' and resid 274 through 276 removed outlier: 4.567A pdb=" N PHE s 274 " --> pdb=" O MET s 92 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 's' and resid 112 through 116 removed outlier: 7.004A pdb=" N ASN s 391 " --> pdb=" O VAL s 113 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU s 115 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS s 393 " --> pdb=" O LEU s 115 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 's' and resid 199 through 202 Processing sheet with id= CB, first strand: chain 's' and resid 214 through 216 Processing sheet with id= CC, first strand: chain 'u' and resid 108 through 113 2115 hydrogen bonds defined for protein. 5955 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 983 hydrogen bonds 1708 hydrogen bond angles 0 basepair planarities 401 basepair parallelities 820 stacking parallelities Total time for adding SS restraints: 56.18 Time building geometry restraints manager: 37.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 12054 1.26 - 1.40: 30577 1.40 - 1.54: 58562 1.54 - 1.68: 3379 1.68 - 1.82: 452 Bond restraints: 105024 Sorted by residual: bond pdb=" CG PRO T 189 " pdb=" CD PRO T 189 " ideal model delta sigma weight residual 1.503 1.141 0.362 3.40e-02 8.65e+02 1.13e+02 bond pdb=" C VAL N 151 " pdb=" N THR N 152 " ideal model delta sigma weight residual 1.332 1.484 -0.153 1.92e-02 2.71e+03 6.32e+01 bond pdb=" C LYS i 68 " pdb=" N HIS i 69 " ideal model delta sigma weight residual 1.333 1.123 0.210 2.74e-02 1.33e+03 5.86e+01 bond pdb=" CB PRO T 189 " pdb=" CG PRO T 189 " ideal model delta sigma weight residual 1.492 1.115 0.377 5.00e-02 4.00e+02 5.67e+01 bond pdb=" C GLU F 194 " pdb=" N LEU F 195 " ideal model delta sigma weight residual 1.325 1.235 0.090 1.25e-02 6.40e+03 5.22e+01 ... (remaining 105019 not shown) Histogram of bond angle deviations from ideal: 76.64 - 91.83: 4 91.83 - 107.03: 14538 107.03 - 122.22: 114877 122.22 - 137.41: 19847 137.41 - 152.60: 9 Bond angle restraints: 149275 Sorted by residual: angle pdb=" N PRO T 189 " pdb=" CD PRO T 189 " pdb=" CG PRO T 189 " ideal model delta sigma weight residual 103.20 76.64 26.56 1.50e+00 4.44e-01 3.13e+02 angle pdb=" C ARG X 36 " pdb=" N THR X 37 " pdb=" CA THR X 37 " ideal model delta sigma weight residual 121.20 143.49 -22.29 1.40e+00 5.10e-01 2.53e+02 angle pdb=" CB PRO T 189 " pdb=" CG PRO T 189 " pdb=" CD PRO T 189 " ideal model delta sigma weight residual 106.10 152.60 -46.50 3.20e+00 9.77e-02 2.11e+02 angle pdb=" CA PRO T 189 " pdb=" CB PRO T 189 " pdb=" CG PRO T 189 " ideal model delta sigma weight residual 104.50 79.21 25.29 1.90e+00 2.77e-01 1.77e+02 angle pdb=" C MET r 99 " pdb=" N LEU r 100 " pdb=" CA LEU r 100 " ideal model delta sigma weight residual 120.39 133.41 -13.02 1.39e+00 5.18e-01 8.77e+01 ... (remaining 149270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 60519 35.99 - 71.98: 3821 71.98 - 107.97: 472 107.97 - 143.96: 18 143.96 - 179.95: 56 Dihedral angle restraints: 64886 sinusoidal: 40950 harmonic: 23936 Sorted by residual: dihedral pdb=" C5' C A 495 " pdb=" C4' C A 495 " pdb=" C3' C A 495 " pdb=" O3' C A 495 " ideal model delta sinusoidal sigma weight residual 147.00 71.78 75.22 1 8.00e+00 1.56e-02 1.12e+02 dihedral pdb=" C5' A A 135 " pdb=" C4' A A 135 " pdb=" C3' A A 135 " pdb=" O3' A A 135 " ideal model delta sinusoidal sigma weight residual 147.00 76.82 70.18 1 8.00e+00 1.56e-02 9.91e+01 dihedral pdb=" C4' A A 135 " pdb=" C3' A A 135 " pdb=" C2' A A 135 " pdb=" C1' A A 135 " ideal model delta sinusoidal sigma weight residual -35.00 33.39 -68.39 1 8.00e+00 1.56e-02 9.48e+01 ... (remaining 64883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 17222 0.199 - 0.398: 313 0.398 - 0.596: 12 0.596 - 0.795: 0 0.795 - 0.994: 2 Chirality restraints: 17549 Sorted by residual: chirality pdb=" CB VAL E 218 " pdb=" CA VAL E 218 " pdb=" CG1 VAL E 218 " pdb=" CG2 VAL E 218 " both_signs ideal model delta sigma weight residual False -2.63 -1.64 -0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CB ILE O 123 " pdb=" CA ILE O 123 " pdb=" CG1 ILE O 123 " pdb=" CG2 ILE O 123 " both_signs ideal model delta sigma weight residual False 2.64 1.83 0.81 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" C3' C A 495 " pdb=" C4' C A 495 " pdb=" O3' C A 495 " pdb=" C2' C A 495 " both_signs ideal model delta sigma weight residual False -2.74 -2.22 -0.52 2.00e-01 2.50e+01 6.82e+00 ... (remaining 17546 not shown) Planarity restraints: 13494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 90 " -0.049 2.00e-02 2.50e+03 4.44e-02 4.92e+01 pdb=" CG TRP E 90 " 0.117 2.00e-02 2.50e+03 pdb=" CD1 TRP E 90 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP E 90 " 0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP E 90 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP E 90 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 90 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 90 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 90 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP E 90 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 224 " -0.022 2.00e-02 2.50e+03 5.03e-02 4.42e+01 pdb=" CG PHE E 224 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE E 224 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE E 224 " 0.093 2.00e-02 2.50e+03 pdb=" CE1 PHE E 224 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE E 224 " -0.030 2.00e-02 2.50e+03 pdb=" CZ PHE E 224 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 237 " -0.077 2.00e-02 2.50e+03 3.49e-02 3.35e+01 pdb=" N9 A A 237 " 0.078 2.00e-02 2.50e+03 pdb=" C8 A A 237 " 0.014 2.00e-02 2.50e+03 pdb=" N7 A A 237 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A A 237 " -0.006 2.00e-02 2.50e+03 pdb=" C6 A A 237 " -0.007 2.00e-02 2.50e+03 pdb=" N6 A A 237 " -0.026 2.00e-02 2.50e+03 pdb=" N1 A A 237 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A A 237 " 0.014 2.00e-02 2.50e+03 pdb=" N3 A A 237 " 0.008 2.00e-02 2.50e+03 pdb=" C4 A A 237 " 0.001 2.00e-02 2.50e+03 ... (remaining 13491 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 2825 2.62 - 3.19: 81818 3.19 - 3.76: 173980 3.76 - 4.33: 238112 4.33 - 4.90: 358397 Nonbonded interactions: 855132 Sorted by model distance: nonbonded pdb=" O LYS X 96 " pdb=" O2' U A 58 " model vdw 2.055 2.440 nonbonded pdb=" O2' C A 408 " pdb=" O2 C A 409 " model vdw 2.082 2.440 nonbonded pdb=" O4 U A 360 " pdb=" N1 A A 454 " model vdw 2.120 3.120 nonbonded pdb=" OG SER F 160 " pdb=" O TRP i 83 " model vdw 2.142 2.440 nonbonded pdb=" OD1 ASN D 194 " pdb=" OG1 THR D 243 " model vdw 2.145 2.440 ... (remaining 855127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 13.290 Check model and map are aligned: 1.080 Set scattering table: 0.690 Process input model: 249.680 Find NCS groups from input model: 2.790 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 273.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 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 : 0.016 0.377 105024 Z= 1.013 Angle : 1.438 46.505 149275 Z= 0.732 Chirality : 0.075 0.994 17549 Planarity : 0.009 0.141 13494 Dihedral : 20.710 179.948 49380 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.64 % Favored : 93.34 % Rotamer: Outliers : 0.03 % Allowed : 0.80 % Favored : 99.17 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.20 (0.09), residues: 8059 helix: -1.32 (0.09), residues: 2655 sheet: -1.38 (0.15), residues: 987 loop : -1.54 (0.09), residues: 4417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.117 0.005 TRP E 90 HIS 0.020 0.003 HIS M 53 PHE 0.093 0.005 PHE E 224 TYR 0.062 0.004 TYR Q 125 ARG 0.054 0.002 ARG 3 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1210 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1208 time to evaluate : 6.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 114 VAL cc_start: 0.8536 (t) cc_final: 0.8333 (t) REVERT: M 28 LYS cc_start: 0.8460 (ttpt) cc_final: 0.7993 (tttp) REVERT: M 106 ASP cc_start: 0.7420 (t0) cc_final: 0.7195 (t0) REVERT: M 155 GLU cc_start: 0.7238 (tp30) cc_final: 0.6982 (tp30) REVERT: M 253 PHE cc_start: 0.8127 (t80) cc_final: 0.7855 (t80) REVERT: N 249 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8376 (pttm) REVERT: P 96 HIS cc_start: 0.8180 (t70) cc_final: 0.7830 (t-90) REVERT: S 157 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7527 (mt-10) REVERT: V 23 MET cc_start: 0.2609 (pmm) cc_final: 0.2200 (pmm) REVERT: V 41 ARG cc_start: 0.4246 (mtp180) cc_final: 0.3631 (mtt-85) REVERT: V 108 MET cc_start: 0.2372 (mtt) cc_final: 0.2048 (mtt) REVERT: V 204 ILE cc_start: 0.7028 (mt) cc_final: 0.6746 (mt) REVERT: X 118 ILE cc_start: 0.8589 (mm) cc_final: 0.8287 (mm) REVERT: X 152 ASP cc_start: 0.8109 (t70) cc_final: 0.7832 (t0) REVERT: Y 139 MET cc_start: 0.7305 (mmt) cc_final: 0.6977 (mmt) REVERT: Z 82 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7736 (mt-10) REVERT: 2 68 ARG cc_start: 0.7652 (ttt90) cc_final: 0.7400 (ttm-80) REVERT: 6 263 SER cc_start: 0.8758 (p) cc_final: 0.8402 (t) REVERT: c 89 LYS cc_start: 0.7359 (mttt) cc_final: 0.6989 (mttt) REVERT: d 232 MET cc_start: 0.7246 (mmm) cc_final: 0.7038 (mmm) REVERT: g 91 MET cc_start: 0.7865 (mmm) cc_final: 0.7545 (mmm) REVERT: j 63 GLN cc_start: 0.8457 (mt0) cc_final: 0.8239 (mt0) REVERT: q 102 SER cc_start: 0.7683 (p) cc_final: 0.7259 (p) REVERT: u 135 LEU cc_start: 0.7965 (mt) cc_final: 0.7708 (mt) REVERT: u 138 MET cc_start: 0.5716 (mtp) cc_final: 0.5216 (ttm) outliers start: 2 outliers final: 0 residues processed: 1209 average time/residue: 0.9304 time to fit residues: 1912.3598 Evaluate side-chains 1034 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1034 time to evaluate : 6.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 800 optimal weight: 0.9980 chunk 718 optimal weight: 8.9990 chunk 398 optimal weight: 0.8980 chunk 245 optimal weight: 0.9980 chunk 484 optimal weight: 50.0000 chunk 383 optimal weight: 0.8980 chunk 743 optimal weight: 10.0000 chunk 287 optimal weight: 1.9990 chunk 451 optimal weight: 8.9990 chunk 553 optimal weight: 20.0000 chunk 860 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN E 52 HIS E 280 HIS F 98 GLN I 45 GLN I 61 HIS I 150 HIS L 43 ASN ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 176 GLN Q 139 GLN ** Q 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 75 HIS S 84 ASN S 118 ASN T 109 ASN ** T 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 16 GLN U 55 ASN ** V 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN Z 150 HIS ** 0 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 82 ASN ** 7 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 198 ASN 7 255 HIS 8 143 GLN 9 113 ASN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 129 GLN c 310 ASN ** d 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN j 30 GLN l 130 ASN ** p 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 79 HIS ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 105024 Z= 0.191 Angle : 0.688 15.112 149275 Z= 0.349 Chirality : 0.042 0.327 17549 Planarity : 0.005 0.080 13494 Dihedral : 22.061 179.946 32006 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.23 % Allowed : 8.95 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.09), residues: 8059 helix: -0.32 (0.10), residues: 2660 sheet: -1.21 (0.16), residues: 955 loop : -1.21 (0.09), residues: 4444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP E 90 HIS 0.010 0.001 HIS I 114 PHE 0.028 0.001 PHE E 224 TYR 0.027 0.002 TYR 5 283 ARG 0.012 0.001 ARG 3 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1247 time to evaluate : 6.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 96 LEU cc_start: 0.7380 (mt) cc_final: 0.7090 (mp) REVERT: I 37 ARG cc_start: 0.7036 (ttm170) cc_final: 0.6754 (ttm-80) REVERT: K 176 TYR cc_start: 0.7421 (t80) cc_final: 0.7200 (t80) REVERT: L 83 LYS cc_start: 0.8654 (mmmm) cc_final: 0.7968 (mppt) REVERT: M 28 LYS cc_start: 0.8321 (ttpt) cc_final: 0.7920 (tttp) REVERT: M 186 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8717 (mp) REVERT: M 233 ARG cc_start: 0.7988 (mtp-110) cc_final: 0.7710 (mtp180) REVERT: M 253 PHE cc_start: 0.8029 (t80) cc_final: 0.7816 (t80) REVERT: M 255 MET cc_start: 0.6901 (tmm) cc_final: 0.6308 (tmm) REVERT: N 118 MET cc_start: 0.7123 (mpp) cc_final: 0.6817 (ptp) REVERT: P 96 HIS cc_start: 0.7916 (t70) cc_final: 0.7664 (t70) REVERT: Q 234 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6554 (pt0) REVERT: S 92 TYR cc_start: 0.7804 (p90) cc_final: 0.7558 (p90) REVERT: T 58 VAL cc_start: 0.8993 (t) cc_final: 0.8681 (m) REVERT: V 23 MET cc_start: 0.2581 (pmm) cc_final: 0.1877 (pmm) REVERT: V 108 MET cc_start: 0.2409 (mtt) cc_final: 0.1786 (mtt) REVERT: V 126 MET cc_start: 0.5539 (pmm) cc_final: 0.4471 (ptp) REVERT: X 118 ILE cc_start: 0.8611 (mm) cc_final: 0.8206 (mm) REVERT: X 152 ASP cc_start: 0.8184 (t70) cc_final: 0.7852 (t0) REVERT: Y 115 LEU cc_start: 0.8296 (tp) cc_final: 0.7969 (tp) REVERT: 3 187 LYS cc_start: 0.7260 (pttp) cc_final: 0.7052 (pttt) REVERT: 5 185 ILE cc_start: 0.7964 (mt) cc_final: 0.7674 (mt) REVERT: 5 254 GLU cc_start: 0.6558 (mp0) cc_final: 0.5787 (pp20) REVERT: 5 418 TYR cc_start: 0.7081 (t80) cc_final: 0.6615 (t80) REVERT: 6 72 ARG cc_start: 0.8096 (mmp80) cc_final: 0.7311 (mmt-90) REVERT: 6 263 SER cc_start: 0.8253 (p) cc_final: 0.7852 (t) REVERT: 7 279 GLU cc_start: 0.6492 (mm-30) cc_final: 0.6092 (mm-30) REVERT: d 159 ARG cc_start: 0.6460 (pmt170) cc_final: 0.6214 (ptt-90) REVERT: d 233 TYR cc_start: 0.6662 (t80) cc_final: 0.6406 (t80) REVERT: e 200 MET cc_start: -0.2640 (ttt) cc_final: -0.3030 (ttt) REVERT: g 91 MET cc_start: 0.7824 (mmm) cc_final: 0.7581 (mmm) REVERT: i 67 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6566 (mm-30) outliers start: 89 outliers final: 49 residues processed: 1287 average time/residue: 0.9390 time to fit residues: 2055.1952 Evaluate side-chains 1136 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1085 time to evaluate : 6.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain J residue 30 MET Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 118 ASN Chi-restraints excluded: chain U residue 16 GLN Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain V residue 190 CYS Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 212 ILE Chi-restraints excluded: chain 0 residue 115 HIS Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 197 SER Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 5 residue 379 ASP Chi-restraints excluded: chain 6 residue 130 VAL Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 9 residue 61 VAL Chi-restraints excluded: chain 9 residue 113 ASN Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 281 ILE Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain s residue 153 GLU Chi-restraints excluded: chain s residue 183 THR Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 297 THR Chi-restraints excluded: chain w residue 120 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 478 optimal weight: 7.9990 chunk 267 optimal weight: 4.9990 chunk 716 optimal weight: 40.0000 chunk 586 optimal weight: 0.0030 chunk 237 optimal weight: 6.9990 chunk 862 optimal weight: 9.9990 chunk 931 optimal weight: 6.9990 chunk 768 optimal weight: 2.9990 chunk 855 optimal weight: 6.9990 chunk 294 optimal weight: 0.0030 chunk 691 optimal weight: 0.9980 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 GLN O 91 GLN ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN S 118 ASN ** T 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 63 GLN ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 277 GLN 8 143 GLN 9 113 ASN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 94 ASN ** d 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 114 ASN k 19 GLN ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 105024 Z= 0.238 Angle : 0.653 11.655 149275 Z= 0.330 Chirality : 0.042 0.302 17549 Planarity : 0.005 0.068 13494 Dihedral : 21.814 179.554 32006 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.02 % Allowed : 11.99 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.09), residues: 8059 helix: 0.07 (0.10), residues: 2668 sheet: -1.16 (0.16), residues: 1001 loop : -1.04 (0.09), residues: 4390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 90 HIS 0.021 0.001 HIS w 103 PHE 0.035 0.001 PHE E 224 TYR 0.026 0.001 TYR v 31 ARG 0.009 0.000 ARG p 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1258 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1112 time to evaluate : 6.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 LYS cc_start: 0.7494 (mttt) cc_final: 0.7001 (mttt) REVERT: F 190 MET cc_start: 0.7784 (mmt) cc_final: 0.7212 (mmt) REVERT: H 96 LEU cc_start: 0.7299 (mt) cc_final: 0.7009 (mp) REVERT: I 95 MET cc_start: 0.3343 (pmm) cc_final: 0.3108 (pmm) REVERT: K 176 TYR cc_start: 0.7487 (t80) cc_final: 0.7237 (t80) REVERT: L 83 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8070 (mppt) REVERT: M 28 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8025 (tttp) REVERT: M 88 SER cc_start: 0.8717 (p) cc_final: 0.8421 (t) REVERT: M 186 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8694 (mp) REVERT: M 254 LYS cc_start: 0.7293 (mmmt) cc_final: 0.6621 (mmtt) REVERT: M 255 MET cc_start: 0.6992 (tmm) cc_final: 0.6714 (tmm) REVERT: M 277 MET cc_start: 0.8076 (tpp) cc_final: 0.7762 (ttt) REVERT: Q 234 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6431 (pt0) REVERT: S 92 TYR cc_start: 0.7928 (p90) cc_final: 0.7652 (p90) REVERT: T 58 VAL cc_start: 0.8961 (t) cc_final: 0.8666 (m) REVERT: V 23 MET cc_start: 0.2685 (pmm) cc_final: 0.1943 (pmm) REVERT: V 108 MET cc_start: 0.2767 (OUTLIER) cc_final: 0.2475 (mtt) REVERT: V 126 MET cc_start: 0.5466 (pmm) cc_final: 0.4420 (ptt) REVERT: X 118 ILE cc_start: 0.8623 (mm) cc_final: 0.8274 (mm) REVERT: X 152 ASP cc_start: 0.8238 (t70) cc_final: 0.7864 (t0) REVERT: Y 111 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.6969 (ttp) REVERT: 5 185 ILE cc_start: 0.7964 (mt) cc_final: 0.7697 (mt) REVERT: 5 192 ILE cc_start: 0.6747 (OUTLIER) cc_final: 0.6243 (tt) REVERT: 5 254 GLU cc_start: 0.6589 (mp0) cc_final: 0.6190 (pp20) REVERT: 6 263 SER cc_start: 0.8408 (p) cc_final: 0.8039 (t) REVERT: 7 279 GLU cc_start: 0.6525 (mm-30) cc_final: 0.6049 (mm-30) REVERT: b 78 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7619 (mt-10) REVERT: e 200 MET cc_start: -0.3032 (ttt) cc_final: -0.3326 (ttt) REVERT: g 91 MET cc_start: 0.7837 (mmm) cc_final: 0.7424 (mmm) REVERT: h 92 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6637 (mt-10) REVERT: i 67 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6604 (mm-30) REVERT: p 98 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8278 (tttt) outliers start: 146 outliers final: 92 residues processed: 1190 average time/residue: 0.9274 time to fit residues: 1888.1695 Evaluate side-chains 1160 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1063 time to evaluate : 7.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 228 GLN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 108 MET Chi-restraints excluded: chain V residue 190 CYS Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain 0 residue 115 HIS Chi-restraints excluded: chain 3 residue 98 SER Chi-restraints excluded: chain 3 residue 188 VAL Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 5 residue 59 THR Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 153 CYS Chi-restraints excluded: chain 5 residue 175 THR Chi-restraints excluded: chain 5 residue 192 ILE Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 5 residue 307 ASP Chi-restraints excluded: chain 6 residue 130 VAL Chi-restraints excluded: chain 6 residue 221 LEU Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 81 MET Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 224 LYS Chi-restraints excluded: chain 9 residue 61 VAL Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain c residue 281 ILE Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain d residue 175 ASP Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 146 THR Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 226 ILE Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 297 THR Chi-restraints excluded: chain s residue 362 THR Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain v residue 52 GLU Chi-restraints excluded: chain w residue 120 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 852 optimal weight: 6.9990 chunk 648 optimal weight: 7.9990 chunk 447 optimal weight: 20.0000 chunk 95 optimal weight: 40.0000 chunk 411 optimal weight: 7.9990 chunk 579 optimal weight: 30.0000 chunk 865 optimal weight: 20.0000 chunk 916 optimal weight: 9.9990 chunk 452 optimal weight: 9.9990 chunk 820 optimal weight: 5.9990 chunk 246 optimal weight: 0.6980 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN F 74 GLN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 75 HIS S 84 ASN S 118 ASN T 109 ASN T 210 HIS ** V 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN ** 7 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 198 ASN 9 113 ASN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 61 HIS h 103 HIS ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 65 ASN ** r 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 152 GLN ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.095 105024 Z= 0.591 Angle : 0.869 12.457 149275 Z= 0.430 Chirality : 0.052 0.395 17549 Planarity : 0.007 0.122 13494 Dihedral : 21.921 179.944 32006 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.26 % Allowed : 14.05 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.09), residues: 8059 helix: -0.04 (0.10), residues: 2685 sheet: -1.14 (0.16), residues: 1005 loop : -1.18 (0.09), residues: 4369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 90 HIS 0.010 0.002 HIS M 53 PHE 0.048 0.002 PHE E 224 TYR 0.027 0.002 TYR 5 176 ARG 0.015 0.001 ARG K 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1096 time to evaluate : 6.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 LYS cc_start: 0.7641 (mttt) cc_final: 0.6966 (mtmt) REVERT: F 81 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7371 (p0) REVERT: F 190 MET cc_start: 0.8019 (mmt) cc_final: 0.7509 (mmt) REVERT: F 243 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8315 (mt) REVERT: H 96 LEU cc_start: 0.7417 (mt) cc_final: 0.7193 (mp) REVERT: H 116 LYS cc_start: 0.7696 (mmmm) cc_final: 0.7320 (mmmm) REVERT: M 186 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8762 (mp) REVERT: M 277 MET cc_start: 0.8138 (tpp) cc_final: 0.7858 (ttt) REVERT: N 249 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8433 (pttm) REVERT: P 96 HIS cc_start: 0.8045 (t-90) cc_final: 0.7691 (t-90) REVERT: Q 234 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6674 (pt0) REVERT: R 11 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7679 (tmt-80) REVERT: R 109 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: T 130 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7081 (ptp-170) REVERT: T 156 ILE cc_start: 0.5935 (OUTLIER) cc_final: 0.5299 (mp) REVERT: V 23 MET cc_start: 0.2716 (pmm) cc_final: 0.1906 (pmm) REVERT: V 126 MET cc_start: 0.5554 (pmm) cc_final: 0.4899 (ptt) REVERT: W 72 HIS cc_start: 0.8633 (OUTLIER) cc_final: 0.8225 (m90) REVERT: W 85 LYS cc_start: 0.8725 (mttm) cc_final: 0.8326 (mmtt) REVERT: X 83 GLU cc_start: 0.7268 (pt0) cc_final: 0.6712 (pt0) REVERT: X 118 ILE cc_start: 0.8641 (mm) cc_final: 0.8339 (mm) REVERT: X 152 ASP cc_start: 0.8298 (t70) cc_final: 0.7827 (t0) REVERT: Y 111 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7002 (ttp) REVERT: 0 120 HIS cc_start: 0.7267 (p-80) cc_final: 0.6684 (p-80) REVERT: 0 185 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: 5 49 VAL cc_start: 0.9332 (OUTLIER) cc_final: 0.9120 (t) REVERT: 5 254 GLU cc_start: 0.6704 (mp0) cc_final: 0.6390 (pp20) REVERT: 6 263 SER cc_start: 0.8645 (p) cc_final: 0.8430 (t) REVERT: 6 379 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7636 (tt) REVERT: 7 279 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6113 (mm-30) REVERT: c 89 LYS cc_start: 0.7403 (mttt) cc_final: 0.7094 (mttt) REVERT: e 200 MET cc_start: -0.3042 (ttt) cc_final: -0.3393 (ttt) REVERT: g 91 MET cc_start: 0.7837 (mmm) cc_final: 0.7263 (mmm) REVERT: g 100 ILE cc_start: 0.7872 (mt) cc_final: 0.7413 (mt) REVERT: g 101 THR cc_start: 0.8841 (t) cc_final: 0.8580 (p) REVERT: h 92 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6660 (mt-10) REVERT: i 57 TYR cc_start: 0.8822 (m-80) cc_final: 0.8519 (m-10) REVERT: i 67 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6695 (mm-30) REVERT: q 51 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7261 (mt0) REVERT: r 85 ASP cc_start: 0.8016 (p0) cc_final: 0.7797 (p0) outliers start: 236 outliers final: 153 residues processed: 1234 average time/residue: 0.9331 time to fit residues: 1966.1125 Evaluate side-chains 1225 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1058 time to evaluate : 6.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 224 PHE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 228 GLN Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain M residue 258 THR Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 11 ARG Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 118 ASN Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 98 SER Chi-restraints excluded: chain T residue 130 ARG Chi-restraints excluded: chain T residue 156 ILE Chi-restraints excluded: chain T residue 166 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 172 ASP Chi-restraints excluded: chain V residue 190 CYS Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 41 VAL Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 176 LEU Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Y residue 177 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain 0 residue 115 HIS Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 3 residue 98 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 188 VAL Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 4 residue 78 ASP Chi-restraints excluded: chain 5 residue 49 VAL Chi-restraints excluded: chain 5 residue 59 THR Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 153 CYS Chi-restraints excluded: chain 5 residue 175 THR Chi-restraints excluded: chain 5 residue 192 ILE Chi-restraints excluded: chain 5 residue 214 ASN Chi-restraints excluded: chain 5 residue 264 ASP Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 6 residue 130 VAL Chi-restraints excluded: chain 6 residue 221 LEU Chi-restraints excluded: chain 6 residue 238 THR Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 379 ILE Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 81 MET Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 274 ILE Chi-restraints excluded: chain 9 residue 61 VAL Chi-restraints excluded: chain 9 residue 113 ASN Chi-restraints excluded: chain a residue 45 CYS Chi-restraints excluded: chain a residue 53 SER Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 61 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 84 SER Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain c residue 276 CYS Chi-restraints excluded: chain c residue 281 ILE Chi-restraints excluded: chain d residue 57 MET Chi-restraints excluded: chain d residue 78 LEU 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 279 THR Chi-restraints excluded: chain e residue 80 GLU Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 107 MET Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 146 THR Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain r residue 172 VAL Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 70 VAL Chi-restraints excluded: chain s residue 149 CYS Chi-restraints excluded: chain s residue 183 THR Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 226 ILE Chi-restraints excluded: chain s residue 227 ASP Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 297 THR Chi-restraints excluded: chain s residue 420 GLN Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 135 LEU Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain w residue 120 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 763 optimal weight: 0.9980 chunk 520 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 682 optimal weight: 50.0000 chunk 378 optimal weight: 0.9980 chunk 781 optimal weight: 5.9990 chunk 633 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 467 optimal weight: 7.9990 chunk 822 optimal weight: 9.9990 chunk 231 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN F 58 HIS F 74 GLN F 105 ASN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 GLN J 41 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN T 109 ASN ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN 5 156 ASN ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 143 GLN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 153 HIS k 19 GLN ** r 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 152 GLN ** s 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 105024 Z= 0.170 Angle : 0.623 15.241 149275 Z= 0.314 Chirality : 0.040 0.337 17549 Planarity : 0.005 0.059 13494 Dihedral : 21.726 179.627 32006 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.47 % Allowed : 15.86 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.78 (0.09), residues: 8059 helix: 0.43 (0.10), residues: 2669 sheet: -1.04 (0.16), residues: 1031 loop : -0.95 (0.09), residues: 4359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP d 183 HIS 0.011 0.001 HIS f 61 PHE 0.033 0.001 PHE 6 318 TYR 0.024 0.001 TYR 5 283 ARG 0.010 0.000 ARG p 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1133 time to evaluate : 6.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 190 MET cc_start: 0.7768 (mmt) cc_final: 0.7277 (mmt) REVERT: F 205 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6698 (mm-30) REVERT: H 76 ARG cc_start: 0.8796 (ptt-90) cc_final: 0.8466 (ptt-90) REVERT: H 96 LEU cc_start: 0.7319 (mt) cc_final: 0.7101 (mp) REVERT: K 176 TYR cc_start: 0.7588 (t80) cc_final: 0.7373 (t80) REVERT: M 186 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8692 (mp) REVERT: M 254 LYS cc_start: 0.7406 (mmmt) cc_final: 0.6658 (mmtt) REVERT: M 255 MET cc_start: 0.6720 (tmm) cc_final: 0.6463 (tmm) REVERT: M 277 MET cc_start: 0.7970 (tpp) cc_final: 0.7756 (ttt) REVERT: O 14 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8965 (t) REVERT: P 96 HIS cc_start: 0.7808 (t-90) cc_final: 0.7428 (t-90) REVERT: S 92 TYR cc_start: 0.7890 (p90) cc_final: 0.7591 (p90) REVERT: T 107 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6939 (mm-30) REVERT: T 130 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7154 (ptp-170) REVERT: T 201 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7046 (tm-30) REVERT: V 23 MET cc_start: 0.3244 (pmm) cc_final: 0.2409 (pmm) REVERT: V 126 MET cc_start: 0.5622 (pmm) cc_final: 0.4987 (ptt) REVERT: X 9 TRP cc_start: 0.7851 (p-90) cc_final: 0.7498 (p-90) REVERT: X 152 ASP cc_start: 0.8235 (t70) cc_final: 0.7831 (t0) REVERT: Y 111 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.6935 (ttp) REVERT: 0 185 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: 5 49 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.9033 (t) REVERT: 5 254 GLU cc_start: 0.6539 (mp0) cc_final: 0.6317 (pp20) REVERT: 6 72 ARG cc_start: 0.8107 (mmp80) cc_final: 0.7370 (mmt180) REVERT: 6 263 SER cc_start: 0.8354 (p) cc_final: 0.8079 (t) REVERT: 7 175 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8006 (mp) REVERT: 7 279 GLU cc_start: 0.6513 (mm-30) cc_final: 0.6053 (mm-30) REVERT: 9 116 LYS cc_start: 0.7344 (ptpp) cc_final: 0.7042 (mtmm) REVERT: e 200 MET cc_start: -0.3046 (ttt) cc_final: -0.3426 (ttt) REVERT: g 91 MET cc_start: 0.7822 (mmm) cc_final: 0.7349 (mmm) REVERT: g 100 ILE cc_start: 0.7796 (mt) cc_final: 0.7370 (mt) REVERT: h 92 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6578 (mt-10) REVERT: h 151 ASN cc_start: 0.9190 (p0) cc_final: 0.8743 (p0) REVERT: i 36 LEU cc_start: 0.8069 (mm) cc_final: 0.7807 (tt) REVERT: i 67 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6584 (mm-30) REVERT: p 98 LYS cc_start: 0.8318 (ttmt) cc_final: 0.8096 (tttt) REVERT: q 51 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6956 (mt0) REVERT: r 85 ASP cc_start: 0.7749 (p0) cc_final: 0.7505 (p0) outliers start: 179 outliers final: 105 residues processed: 1235 average time/residue: 0.9285 time to fit residues: 1954.6854 Evaluate side-chains 1190 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1076 time to evaluate : 8.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 74 GLN Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 228 GLN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain O residue 14 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain Q residue 290 LYS Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain T residue 109 ASN Chi-restraints excluded: chain T residue 130 ARG Chi-restraints excluded: chain T residue 201 GLN Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 190 CYS Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 41 VAL Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain 0 residue 115 HIS Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 188 VAL Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 5 residue 49 VAL Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 175 THR Chi-restraints excluded: chain 5 residue 192 ILE Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 5 residue 307 ASP Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 6 residue 130 VAL Chi-restraints excluded: chain 6 residue 221 LEU Chi-restraints excluded: chain 6 residue 301 PHE Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 81 MET Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 175 ILE Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 9 residue 61 VAL Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 84 SER Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 176 GLU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain c residue 281 ILE Chi-restraints excluded: chain d residue 57 MET Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 237 ASP Chi-restraints excluded: chain e residue 80 GLU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain o residue 35 MET Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 105 THR Chi-restraints excluded: chain s residue 149 CYS Chi-restraints excluded: chain s residue 183 THR Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 226 ILE Chi-restraints excluded: chain s residue 227 ASP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 297 THR Chi-restraints excluded: chain s residue 420 GLN Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 135 LEU Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain w residue 120 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 308 optimal weight: 20.0000 chunk 825 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 538 optimal weight: 5.9990 chunk 226 optimal weight: 0.0050 chunk 917 optimal weight: 20.0000 chunk 761 optimal weight: 0.9980 chunk 424 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 303 optimal weight: 30.0000 chunk 481 optimal weight: 0.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN F 74 GLN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN T 109 ASN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 GLN ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 198 ASN 7 298 GLN 9 113 ASN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 103 HIS h 114 ASN ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 105024 Z= 0.295 Angle : 0.661 12.353 149275 Z= 0.331 Chirality : 0.042 0.341 17549 Planarity : 0.005 0.084 13494 Dihedral : 21.637 179.716 32006 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.79 % Allowed : 16.62 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % 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: -0.71 (0.09), residues: 8059 helix: 0.50 (0.10), residues: 2675 sheet: -1.00 (0.16), residues: 1035 loop : -0.92 (0.09), residues: 4349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP s 66 HIS 0.011 0.001 HIS f 61 PHE 0.038 0.002 PHE E 224 TYR 0.024 0.002 TYR 5 176 ARG 0.020 0.000 ARG q 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1103 time to evaluate : 6.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 190 MET cc_start: 0.7842 (mmt) cc_final: 0.7355 (mmt) REVERT: F 205 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6898 (mm-30) REVERT: H 96 LEU cc_start: 0.7388 (mt) cc_final: 0.7151 (mp) REVERT: M 186 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8697 (mp) REVERT: M 254 LYS cc_start: 0.7504 (mmmt) cc_final: 0.6727 (mmtp) REVERT: M 255 MET cc_start: 0.6909 (tmm) cc_final: 0.6454 (tmm) REVERT: N 83 THR cc_start: 0.6777 (OUTLIER) cc_final: 0.6551 (t) REVERT: O 13 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.7008 (mmt90) REVERT: P 96 HIS cc_start: 0.7853 (t-90) cc_final: 0.7486 (t-90) REVERT: T 107 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7130 (mm-30) REVERT: T 110 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7698 (t0) REVERT: T 201 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: V 23 MET cc_start: 0.3230 (pmm) cc_final: 0.2327 (pmm) REVERT: V 126 MET cc_start: 0.5618 (pmm) cc_final: 0.4995 (ptt) REVERT: W 85 LYS cc_start: 0.8615 (mttm) cc_final: 0.8188 (mmtt) REVERT: X 9 TRP cc_start: 0.7883 (p-90) cc_final: 0.7524 (p-90) REVERT: X 152 ASP cc_start: 0.8262 (t70) cc_final: 0.7843 (t0) REVERT: Y 111 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.6952 (ttp) REVERT: 0 185 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: 5 49 VAL cc_start: 0.9274 (OUTLIER) cc_final: 0.9013 (t) REVERT: 5 254 GLU cc_start: 0.6547 (mp0) cc_final: 0.6262 (pp20) REVERT: 6 263 SER cc_start: 0.8451 (p) cc_final: 0.8181 (t) REVERT: 6 379 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7202 (tt) REVERT: 7 175 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8044 (mp) REVERT: c 49 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.5983 (ttp-170) REVERT: c 89 LYS cc_start: 0.7304 (mttt) cc_final: 0.7010 (mttt) REVERT: e 200 MET cc_start: -0.3062 (ttt) cc_final: -0.3460 (ttt) REVERT: g 91 MET cc_start: 0.7997 (mmm) cc_final: 0.7156 (mmm) REVERT: g 100 ILE cc_start: 0.7914 (mt) cc_final: 0.7484 (mt) REVERT: g 101 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8609 (p) REVERT: h 92 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6561 (mt-10) REVERT: h 151 ASN cc_start: 0.9217 (p0) cc_final: 0.8776 (p0) REVERT: i 36 LEU cc_start: 0.8217 (mm) cc_final: 0.7894 (tt) REVERT: i 67 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6651 (mm-30) REVERT: o 54 MET cc_start: 0.8157 (mtp) cc_final: 0.7879 (mtt) REVERT: p 98 LYS cc_start: 0.8361 (ttmt) cc_final: 0.8158 (tttt) REVERT: p 175 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6260 (mm) REVERT: r 85 ASP cc_start: 0.7857 (p0) cc_final: 0.7434 (p0) outliers start: 202 outliers final: 141 residues processed: 1219 average time/residue: 0.9275 time to fit residues: 1936.9154 Evaluate side-chains 1232 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1078 time to evaluate : 6.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 224 PHE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 228 GLN Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain M residue 258 THR Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain T residue 110 ASP Chi-restraints excluded: chain T residue 167 MET Chi-restraints excluded: chain T residue 201 GLN Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 190 CYS Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 41 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Y residue 177 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain 0 residue 115 HIS Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 3 residue 98 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 188 VAL Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 5 residue 49 VAL Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 175 THR Chi-restraints excluded: chain 5 residue 192 ILE Chi-restraints excluded: chain 5 residue 214 ASN Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 5 residue 307 ASP Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 6 residue 130 VAL Chi-restraints excluded: chain 6 residue 238 THR Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 6 residue 379 ILE Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 81 MET Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 149 MET Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 175 ILE Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 275 CYS Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 9 residue 61 VAL Chi-restraints excluded: chain a residue 45 CYS Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 49 ARG Chi-restraints excluded: chain c residue 84 SER Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 176 GLU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain c residue 281 ILE Chi-restraints excluded: chain d residue 57 MET Chi-restraints excluded: chain d residue 78 LEU 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 237 ASP Chi-restraints excluded: chain e residue 80 GLU Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 146 THR Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain o residue 35 MET Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 175 LEU Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain r residue 105 THR Chi-restraints excluded: chain r residue 172 VAL Chi-restraints excluded: chain s residue 70 VAL Chi-restraints excluded: chain s residue 183 THR Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 226 ILE Chi-restraints excluded: chain s residue 227 ASP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 297 THR Chi-restraints excluded: chain s residue 322 VAL Chi-restraints excluded: chain s residue 381 THR Chi-restraints excluded: chain s residue 420 GLN Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 135 LEU Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain w residue 120 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 884 optimal weight: 40.0000 chunk 103 optimal weight: 0.6980 chunk 522 optimal weight: 0.6980 chunk 669 optimal weight: 7.9990 chunk 518 optimal weight: 5.9990 chunk 772 optimal weight: 9.9990 chunk 512 optimal weight: 20.0000 chunk 913 optimal weight: 8.9990 chunk 571 optimal weight: 7.9990 chunk 557 optimal weight: 4.9990 chunk 421 optimal weight: 2.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN F 74 GLN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 210 GLN ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN T 109 ASN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN 8 143 GLN 9 113 ASN c 65 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 103 HIS ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 91 GLN ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 105024 Z= 0.331 Angle : 0.688 13.767 149275 Z= 0.343 Chirality : 0.043 0.378 17549 Planarity : 0.005 0.090 13494 Dihedral : 21.629 179.914 32006 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.19 % Allowed : 16.83 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % 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: -0.70 (0.09), residues: 8059 helix: 0.50 (0.10), residues: 2669 sheet: -0.96 (0.16), residues: 1038 loop : -0.91 (0.09), residues: 4352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP 6 235 HIS 0.011 0.001 HIS f 61 PHE 0.043 0.002 PHE E 224 TYR 0.027 0.002 TYR 6 51 ARG 0.010 0.000 ARG j 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1315 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1084 time to evaluate : 6.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 107 MET cc_start: 0.8357 (ptm) cc_final: 0.8140 (ptm) REVERT: E 125 GLN cc_start: 0.8622 (mt0) cc_final: 0.8375 (mt0) REVERT: F 81 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7273 (p0) REVERT: F 190 MET cc_start: 0.7906 (mmt) cc_final: 0.7401 (mmt) REVERT: F 243 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8211 (mt) REVERT: M 186 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8692 (mp) REVERT: M 255 MET cc_start: 0.6940 (tmm) cc_final: 0.6456 (tmm) REVERT: N 83 THR cc_start: 0.6814 (OUTLIER) cc_final: 0.6586 (t) REVERT: R 109 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: S 94 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8496 (ttm170) REVERT: T 156 ILE cc_start: 0.5744 (OUTLIER) cc_final: 0.5255 (mt) REVERT: T 201 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7151 (tm-30) REVERT: V 23 MET cc_start: 0.3233 (pmm) cc_final: 0.2394 (pmm) REVERT: V 97 TYR cc_start: 0.3436 (OUTLIER) cc_final: 0.1572 (m-80) REVERT: V 126 MET cc_start: 0.5544 (pmm) cc_final: 0.4928 (ptt) REVERT: W 72 HIS cc_start: 0.8572 (OUTLIER) cc_final: 0.8153 (m90) REVERT: W 85 LYS cc_start: 0.8669 (mttm) cc_final: 0.8222 (mmtt) REVERT: X 118 ILE cc_start: 0.8118 (mp) cc_final: 0.7901 (mm) REVERT: X 152 ASP cc_start: 0.8255 (t70) cc_final: 0.7712 (t0) REVERT: Y 111 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.6952 (ttp) REVERT: 0 185 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: 5 106 ILE cc_start: 0.7177 (mm) cc_final: 0.6909 (mm) REVERT: 5 254 GLU cc_start: 0.6749 (mp0) cc_final: 0.5827 (pp20) REVERT: 6 258 PHE cc_start: 0.7692 (p90) cc_final: 0.7433 (p90) REVERT: 6 263 SER cc_start: 0.8549 (p) cc_final: 0.8296 (t) REVERT: 6 379 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7341 (tt) REVERT: 7 175 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8052 (mp) REVERT: 9 116 LYS cc_start: 0.7384 (ptpp) cc_final: 0.6998 (mttp) REVERT: c 49 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6071 (ttp-170) REVERT: e 200 MET cc_start: -0.2998 (ttt) cc_final: -0.3393 (ttt) REVERT: f 127 MET cc_start: 0.1435 (mmm) cc_final: 0.1164 (mmm) REVERT: g 100 ILE cc_start: 0.7884 (mt) cc_final: 0.7497 (mt) REVERT: g 101 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8647 (p) REVERT: h 92 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6559 (mt-10) REVERT: h 151 ASN cc_start: 0.9230 (p0) cc_final: 0.8773 (p0) REVERT: i 36 LEU cc_start: 0.8106 (mm) cc_final: 0.7717 (tp) REVERT: i 67 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6570 (mm-30) REVERT: o 54 MET cc_start: 0.8173 (mtp) cc_final: 0.7943 (mtt) REVERT: p 98 LYS cc_start: 0.8368 (ttmt) cc_final: 0.8150 (tttt) REVERT: p 175 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6301 (mm) REVERT: r 85 ASP cc_start: 0.7782 (p0) cc_final: 0.7432 (p0) REVERT: s 239 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7822 (p0) outliers start: 231 outliers final: 165 residues processed: 1227 average time/residue: 0.9292 time to fit residues: 1953.5013 Evaluate side-chains 1233 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1050 time to evaluate : 6.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 224 PHE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 74 GLN Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 120 ARG Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain M residue 258 THR Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 142 ASN Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 94 ARG Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 98 SER Chi-restraints excluded: chain T residue 156 ILE Chi-restraints excluded: chain T residue 166 ILE Chi-restraints excluded: chain T residue 201 GLN Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 97 TYR Chi-restraints excluded: chain V residue 190 CYS Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 41 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Y residue 177 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain 0 residue 115 HIS Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 3 residue 98 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 188 VAL Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 4 residue 78 ASP Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 175 THR Chi-restraints excluded: chain 5 residue 192 ILE Chi-restraints excluded: chain 5 residue 214 ASN Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 6 residue 130 VAL Chi-restraints excluded: chain 6 residue 238 THR Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 6 residue 379 ILE Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 81 MET Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 149 MET Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 175 ILE Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 275 CYS Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 9 residue 61 VAL Chi-restraints excluded: chain 9 residue 113 ASN Chi-restraints excluded: chain a residue 45 CYS Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 49 ARG Chi-restraints excluded: chain c residue 84 SER Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 176 GLU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain c residue 245 LEU Chi-restraints excluded: chain c residue 281 ILE Chi-restraints excluded: chain d residue 57 MET Chi-restraints excluded: chain d residue 78 LEU 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 e residue 80 GLU Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 146 THR Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 175 LEU Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain r residue 105 THR Chi-restraints excluded: chain r residue 172 VAL Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 70 VAL Chi-restraints excluded: chain s residue 183 THR Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 226 ILE Chi-restraints excluded: chain s residue 227 ASP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 297 THR Chi-restraints excluded: chain s residue 322 VAL Chi-restraints excluded: chain s residue 381 THR Chi-restraints excluded: chain s residue 420 GLN Chi-restraints excluded: chain u residue 94 ILE Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 135 LEU Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain v residue 52 GLU Chi-restraints excluded: chain w residue 120 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 565 optimal weight: 8.9990 chunk 364 optimal weight: 1.9990 chunk 545 optimal weight: 6.9990 chunk 275 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 580 optimal weight: 40.0000 chunk 622 optimal weight: 50.0000 chunk 451 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 718 optimal weight: 50.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN F 74 GLN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN T 109 ASN U 98 GLN ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 113 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 26 GLN ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 105024 Z= 0.211 Angle : 0.622 11.548 149275 Z= 0.312 Chirality : 0.040 0.364 17549 Planarity : 0.005 0.060 13494 Dihedral : 21.544 179.782 32006 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.56 % Allowed : 17.89 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.54 (0.09), residues: 8059 helix: 0.64 (0.10), residues: 2675 sheet: -0.92 (0.16), residues: 1060 loop : -0.81 (0.10), residues: 4324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP N 99 HIS 0.010 0.001 HIS f 61 PHE 0.033 0.001 PHE 6 318 TYR 0.026 0.001 TYR 6 51 ARG 0.010 0.000 ARG p 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1091 time to evaluate : 6.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 190 MET cc_start: 0.7820 (mmt) cc_final: 0.7341 (mmt) REVERT: F 243 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8139 (mt) REVERT: M 186 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8681 (mp) REVERT: M 255 MET cc_start: 0.6922 (tmm) cc_final: 0.6425 (tmm) REVERT: N 83 THR cc_start: 0.6743 (OUTLIER) cc_final: 0.6527 (t) REVERT: T 107 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7151 (mm-30) REVERT: T 149 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7393 (ttt90) REVERT: T 201 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: V 23 MET cc_start: 0.3253 (pmm) cc_final: 0.2394 (pmm) REVERT: V 97 TYR cc_start: 0.3455 (OUTLIER) cc_final: 0.1605 (m-80) REVERT: V 126 MET cc_start: 0.5545 (pmm) cc_final: 0.4992 (ptt) REVERT: V 199 MET cc_start: 0.6437 (tmm) cc_final: 0.6096 (tmm) REVERT: W 72 HIS cc_start: 0.8518 (OUTLIER) cc_final: 0.8063 (m90) REVERT: X 152 ASP cc_start: 0.8209 (t70) cc_final: 0.7796 (t0) REVERT: Y 111 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.6952 (ttp) REVERT: 0 185 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: 5 254 GLU cc_start: 0.6790 (mp0) cc_final: 0.5895 (pp20) REVERT: 6 263 SER cc_start: 0.8415 (p) cc_final: 0.8136 (t) REVERT: 6 379 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7113 (tt) REVERT: 7 93 MET cc_start: 0.6848 (mmt) cc_final: 0.6490 (mmt) REVERT: 7 143 TRP cc_start: 0.7448 (OUTLIER) cc_final: 0.7090 (m-90) REVERT: 7 175 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.7985 (mp) REVERT: c 49 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6013 (ttp-170) REVERT: d 182 ARG cc_start: 0.6803 (mtm-85) cc_final: 0.6518 (mtm180) REVERT: e 200 MET cc_start: -0.3009 (ttt) cc_final: -0.3402 (ttt) REVERT: g 100 ILE cc_start: 0.7863 (mt) cc_final: 0.7458 (mt) REVERT: g 101 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8610 (p) REVERT: h 151 ASN cc_start: 0.9212 (p0) cc_final: 0.8769 (p0) REVERT: i 36 LEU cc_start: 0.8042 (mm) cc_final: 0.7690 (tp) REVERT: i 67 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6593 (mm-30) REVERT: o 54 MET cc_start: 0.8120 (mtp) cc_final: 0.7880 (mtt) REVERT: r 85 ASP cc_start: 0.7788 (p0) cc_final: 0.7582 (p0) REVERT: s 201 ASP cc_start: 0.6437 (m-30) cc_final: 0.6232 (m-30) REVERT: s 239 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7796 (p0) outliers start: 185 outliers final: 138 residues processed: 1200 average time/residue: 0.9725 time to fit residues: 2009.5993 Evaluate side-chains 1202 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1049 time to evaluate : 6.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 74 GLN Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 228 GLN Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 142 ASN Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 94 ARG Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 149 ARG Chi-restraints excluded: chain T residue 166 ILE Chi-restraints excluded: chain T residue 201 GLN Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 97 TYR Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain W residue 142 PHE Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 41 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain 0 residue 115 HIS Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 3 residue 98 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 188 VAL Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 5 residue 59 THR Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 175 THR Chi-restraints excluded: chain 5 residue 192 ILE Chi-restraints excluded: chain 5 residue 214 ASN Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 5 residue 307 ASP Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 6 residue 130 VAL Chi-restraints excluded: chain 6 residue 238 THR Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 6 residue 379 ILE Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 81 MET Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 175 ILE Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 9 residue 61 VAL Chi-restraints excluded: chain 9 residue 113 ASN Chi-restraints excluded: chain a residue 45 CYS Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 49 ARG Chi-restraints excluded: chain c residue 84 SER Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 176 GLU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain c residue 281 ILE Chi-restraints excluded: chain d residue 57 MET Chi-restraints excluded: chain d residue 78 LEU 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 237 ASP Chi-restraints excluded: chain e residue 80 GLU Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain o residue 35 MET Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain r residue 105 THR Chi-restraints excluded: chain r residue 172 VAL Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 89 MET Chi-restraints excluded: chain s residue 183 THR Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 226 ILE Chi-restraints excluded: chain s residue 227 ASP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 297 THR Chi-restraints excluded: chain s residue 381 THR Chi-restraints excluded: chain s residue 420 GLN Chi-restraints excluded: chain u residue 94 ILE Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 135 LEU Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain v residue 52 GLU Chi-restraints excluded: chain w residue 120 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 831 optimal weight: 6.9990 chunk 875 optimal weight: 8.9990 chunk 798 optimal weight: 9.9990 chunk 851 optimal weight: 8.9990 chunk 512 optimal weight: 9.9990 chunk 370 optimal weight: 0.6980 chunk 668 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 769 optimal weight: 10.0000 chunk 805 optimal weight: 5.9990 chunk 848 optimal weight: 50.0000 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN T 109 ASN ** Y 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 113 ASN c 65 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 105024 Z= 0.478 Angle : 0.784 12.598 149275 Z= 0.388 Chirality : 0.048 0.439 17549 Planarity : 0.006 0.117 13494 Dihedral : 21.633 179.981 32006 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.05 % Allowed : 17.97 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % 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: -0.75 (0.09), residues: 8059 helix: 0.43 (0.10), residues: 2672 sheet: -0.89 (0.16), residues: 1010 loop : -0.96 (0.09), residues: 4377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP N 99 HIS 0.010 0.001 HIS f 61 PHE 0.053 0.002 PHE E 224 TYR 0.030 0.002 TYR 9 131 ARG 0.014 0.001 ARG q 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1282 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1061 time to evaluate : 6.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 125 GLN cc_start: 0.8586 (mt0) cc_final: 0.8335 (mt0) REVERT: F 81 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7304 (p0) REVERT: F 190 MET cc_start: 0.8014 (mmt) cc_final: 0.7532 (mmt) REVERT: F 243 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8048 (tt) REVERT: M 186 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8736 (mp) REVERT: M 255 MET cc_start: 0.6994 (tmm) cc_final: 0.6476 (tmm) REVERT: N 83 THR cc_start: 0.6886 (OUTLIER) cc_final: 0.6640 (t) REVERT: N 249 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8316 (pttm) REVERT: R 109 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: S 94 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8445 (ttm170) REVERT: T 149 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7492 (ttt90) REVERT: T 201 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: V 23 MET cc_start: 0.3088 (pmm) cc_final: 0.2104 (pmm) REVERT: V 97 TYR cc_start: 0.3562 (OUTLIER) cc_final: 0.1657 (m-80) REVERT: V 126 MET cc_start: 0.5568 (pmm) cc_final: 0.5031 (ptt) REVERT: W 72 HIS cc_start: 0.8598 (OUTLIER) cc_final: 0.8172 (m90) REVERT: X 9 TRP cc_start: 0.7878 (p-90) cc_final: 0.7494 (p-90) REVERT: X 152 ASP cc_start: 0.8310 (t70) cc_final: 0.7726 (t0) REVERT: Y 111 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.6989 (ttp) REVERT: 0 185 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: 3 130 LYS cc_start: 0.7929 (pttt) cc_final: 0.7723 (pttt) REVERT: 5 254 GLU cc_start: 0.6883 (mp0) cc_final: 0.6010 (pp20) REVERT: 6 258 PHE cc_start: 0.7749 (p90) cc_final: 0.7493 (p90) REVERT: 6 263 SER cc_start: 0.8604 (p) cc_final: 0.8381 (t) REVERT: 6 379 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7588 (tt) REVERT: 7 143 TRP cc_start: 0.7566 (OUTLIER) cc_final: 0.7073 (m-90) REVERT: 7 175 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8094 (mp) REVERT: c 49 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6091 (ttp-170) REVERT: e 200 MET cc_start: -0.2964 (ttt) cc_final: -0.3381 (ttt) REVERT: f 127 MET cc_start: 0.1397 (mmm) cc_final: 0.1123 (mmm) REVERT: g 91 MET cc_start: 0.8102 (mmm) cc_final: 0.7131 (mmm) REVERT: g 100 ILE cc_start: 0.7987 (mt) cc_final: 0.7675 (mt) REVERT: g 101 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8586 (p) REVERT: i 57 TYR cc_start: 0.8800 (m-80) cc_final: 0.8546 (m-10) REVERT: i 67 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6605 (mm-30) REVERT: o 54 MET cc_start: 0.8229 (mtp) cc_final: 0.7973 (mtt) REVERT: r 85 ASP cc_start: 0.7997 (p0) cc_final: 0.7655 (p0) REVERT: s 239 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7833 (p0) outliers start: 221 outliers final: 170 residues processed: 1196 average time/residue: 0.9432 time to fit residues: 1938.6694 Evaluate side-chains 1228 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1040 time to evaluate : 6.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 224 PHE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 74 GLN Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 228 GLN Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain M residue 258 THR Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain M residue 279 ASP Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 142 ASN Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 151 LEU Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 94 ARG Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 98 SER Chi-restraints excluded: chain T residue 149 ARG Chi-restraints excluded: chain T residue 166 ILE Chi-restraints excluded: chain T residue 201 GLN Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 97 TYR Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain W residue 142 PHE Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 41 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Y residue 177 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain 0 residue 106 ASN Chi-restraints excluded: chain 0 residue 115 HIS Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 3 residue 98 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 188 VAL Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 4 residue 78 ASP Chi-restraints excluded: chain 5 residue 59 THR Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 153 CYS Chi-restraints excluded: chain 5 residue 175 THR Chi-restraints excluded: chain 5 residue 192 ILE Chi-restraints excluded: chain 5 residue 214 ASN Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 6 residue 130 VAL Chi-restraints excluded: chain 6 residue 238 THR Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 6 residue 379 ILE Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 81 MET Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 175 ILE Chi-restraints excluded: chain 7 residue 185 LEU Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 9 residue 61 VAL Chi-restraints excluded: chain 9 residue 113 ASN Chi-restraints excluded: chain a residue 45 CYS Chi-restraints excluded: chain a residue 53 SER Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 61 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 49 ARG Chi-restraints excluded: chain c residue 84 SER Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 176 GLU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain c residue 281 ILE Chi-restraints excluded: chain d residue 57 MET Chi-restraints excluded: chain d residue 78 LEU 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 e residue 80 GLU Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain g residue 107 MET Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 146 THR Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain o residue 35 MET Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 153 LYS Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain r residue 105 THR Chi-restraints excluded: chain r residue 172 VAL Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 70 VAL Chi-restraints excluded: chain s residue 183 THR Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 226 ILE Chi-restraints excluded: chain s residue 227 ASP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 297 THR Chi-restraints excluded: chain s residue 381 THR Chi-restraints excluded: chain s residue 420 GLN Chi-restraints excluded: chain u residue 94 ILE Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 135 LEU Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain v residue 52 GLU Chi-restraints excluded: chain w residue 120 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 559 optimal weight: 10.0000 chunk 900 optimal weight: 20.0000 chunk 549 optimal weight: 0.9980 chunk 427 optimal weight: 2.9990 chunk 625 optimal weight: 20.0000 chunk 944 optimal weight: 40.0000 chunk 869 optimal weight: 6.9990 chunk 752 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 580 optimal weight: 0.0060 chunk 461 optimal weight: 7.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 74 GLN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN T 109 ASN ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 113 ASN c 65 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 91 GLN ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 19 GLN ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 105024 Z= 0.195 Angle : 0.627 12.500 149275 Z= 0.314 Chirality : 0.040 0.376 17549 Planarity : 0.005 0.067 13494 Dihedral : 21.522 179.448 32006 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.47 % Allowed : 18.55 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.51 (0.09), residues: 8059 helix: 0.68 (0.10), residues: 2676 sheet: -0.88 (0.16), residues: 1034 loop : -0.80 (0.10), residues: 4349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP N 99 HIS 0.009 0.001 HIS f 61 PHE 0.033 0.001 PHE 6 318 TYR 0.023 0.001 TYR 9 131 ARG 0.014 0.000 ARG q 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1270 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1091 time to evaluate : 7.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 190 MET cc_start: 0.7823 (mmt) cc_final: 0.7369 (mmt) REVERT: F 243 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8134 (mt) REVERT: M 186 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8687 (mp) REVERT: M 255 MET cc_start: 0.7052 (tmm) cc_final: 0.6586 (tmm) REVERT: N 83 THR cc_start: 0.6747 (OUTLIER) cc_final: 0.6534 (t) REVERT: P 96 HIS cc_start: 0.7713 (t-90) cc_final: 0.7447 (t-90) REVERT: Q 224 MET cc_start: 0.7508 (mmm) cc_final: 0.7301 (mmm) REVERT: R 11 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7188 (tmt-80) REVERT: T 149 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7387 (ttt90) REVERT: T 156 ILE cc_start: 0.5663 (OUTLIER) cc_final: 0.5137 (mt) REVERT: T 201 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: V 23 MET cc_start: 0.3477 (pmm) cc_final: 0.2681 (pmm) REVERT: V 97 TYR cc_start: 0.3420 (OUTLIER) cc_final: 0.1547 (m-80) REVERT: V 126 MET cc_start: 0.5600 (pmm) cc_final: 0.4957 (ptt) REVERT: V 199 MET cc_start: 0.6460 (tmm) cc_final: 0.6121 (tmm) REVERT: X 9 TRP cc_start: 0.7820 (p-90) cc_final: 0.7340 (p-90) REVERT: X 152 ASP cc_start: 0.8162 (t70) cc_final: 0.7746 (t0) REVERT: Y 111 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.6903 (ttp) REVERT: 0 185 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: 5 254 GLU cc_start: 0.6895 (mp0) cc_final: 0.5977 (pp20) REVERT: 6 263 SER cc_start: 0.8390 (p) cc_final: 0.8108 (t) REVERT: 7 93 MET cc_start: 0.6820 (mmt) cc_final: 0.6578 (mmt) REVERT: 7 143 TRP cc_start: 0.7526 (OUTLIER) cc_final: 0.7068 (m-90) REVERT: 7 175 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7965 (mp) REVERT: c 49 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6113 (ttp-170) REVERT: d 182 ARG cc_start: 0.6773 (mtm-85) cc_final: 0.6497 (mtm180) REVERT: d 233 TYR cc_start: 0.6378 (t80) cc_final: 0.6146 (t80) REVERT: e 200 MET cc_start: -0.3094 (ttt) cc_final: -0.3485 (ttt) REVERT: f 127 MET cc_start: 0.1317 (mmm) cc_final: 0.1070 (mmm) REVERT: g 100 ILE cc_start: 0.7879 (mt) cc_final: 0.7557 (mt) REVERT: g 101 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8642 (p) REVERT: h 151 ASN cc_start: 0.9194 (p0) cc_final: 0.8763 (p0) REVERT: i 36 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7592 (tp) REVERT: i 67 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6510 (mm-30) REVERT: o 54 MET cc_start: 0.8109 (mtp) cc_final: 0.7879 (mtt) REVERT: p 157 MET cc_start: 0.8061 (tpp) cc_final: 0.7743 (ttm) REVERT: s 239 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7810 (p0) outliers start: 179 outliers final: 141 residues processed: 1198 average time/residue: 0.9489 time to fit residues: 1957.3586 Evaluate side-chains 1213 residues out of total 7261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1056 time to evaluate : 6.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 74 GLN Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain M residue 279 ASP Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 142 ASN Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 11 ARG Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 94 ARG Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 98 SER Chi-restraints excluded: chain T residue 149 ARG Chi-restraints excluded: chain T residue 156 ILE Chi-restraints excluded: chain T residue 201 GLN Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain V residue 97 TYR Chi-restraints excluded: chain V residue 190 CYS Chi-restraints excluded: chain W residue 142 PHE Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 41 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain 0 residue 106 ASN Chi-restraints excluded: chain 0 residue 115 HIS Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 3 residue 98 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 188 VAL Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 5 residue 59 THR Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 153 CYS Chi-restraints excluded: chain 5 residue 175 THR Chi-restraints excluded: chain 5 residue 192 ILE Chi-restraints excluded: chain 5 residue 214 ASN Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 6 residue 130 VAL Chi-restraints excluded: chain 6 residue 238 THR Chi-restraints excluded: chain 6 residue 371 ASP Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 81 MET Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 175 ILE Chi-restraints excluded: chain 7 residue 185 LEU Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 9 residue 61 VAL Chi-restraints excluded: chain 9 residue 113 ASN Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 49 ARG Chi-restraints excluded: chain c residue 84 SER Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 176 GLU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain c residue 281 ILE Chi-restraints excluded: chain d residue 57 MET Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain e residue 80 GLU Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 146 THR Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 132 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 36 LEU Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain l residue 124 GLN Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain r residue 105 THR Chi-restraints excluded: chain r residue 172 VAL Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 183 THR Chi-restraints excluded: chain s residue 216 ILE Chi-restraints excluded: chain s residue 226 ILE Chi-restraints excluded: chain s residue 227 ASP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 297 THR Chi-restraints excluded: chain s residue 322 VAL Chi-restraints excluded: chain s residue 381 THR Chi-restraints excluded: chain s residue 420 GLN Chi-restraints excluded: chain u residue 94 ILE Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 135 LEU Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain v residue 52 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 597 optimal weight: 8.9990 chunk 801 optimal weight: 5.9990 chunk 230 optimal weight: 0.5980 chunk 693 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 208 optimal weight: 0.9980 chunk 753 optimal weight: 0.7980 chunk 315 optimal weight: 5.9990 chunk 773 optimal weight: 4.9990 chunk 95 optimal weight: 50.0000 chunk 138 optimal weight: 8.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN 9 113 ASN c 65 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.186743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.152110 restraints weight = 128036.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.151538 restraints weight = 317421.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.151363 restraints weight = 115951.947| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 105024 Z= 0.298 Angle : 0.672 12.189 149275 Z= 0.335 Chirality : 0.042 0.394 17549 Planarity : 0.005 0.090 13494 Dihedral : 21.489 179.661 32006 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.54 % Allowed : 18.64 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % 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: -0.52 (0.09), residues: 8059 helix: 0.66 (0.10), residues: 2663 sheet: -0.90 (0.16), residues: 1056 loop : -0.80 (0.10), residues: 4340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP N 99 HIS 0.009 0.001 HIS f 61 PHE 0.042 0.002 PHE E 224 TYR 0.044 0.002 TYR 5 283 ARG 0.012 0.000 ARG c 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26058.91 seconds wall clock time: 458 minutes 6.87 seconds (27486.87 seconds total)